A native of Ireland, Hughes was born and raised in the south of County Tyrone. He emigrated to the United States in 1817, and became a priest in 1826 and a bishop in 1838. A figure of national prominence, he exercised great moral and social influence, and presided over a period of explosive growth for Catholicism in New York. He was regarded as "the best known, if not exactly the best loved, Catholic bishop in the country." He became known as "Dagger John", both for his following the Catholic practice wherein a bishop precedes his signature with a cross, as well as for his aggressive personality.
Hughes was born in the hamlet of Annaloghan, near Aughnacloy, in County Tyrone, part of the Province of Ulster in the north of Ireland. He was the third of seven children of Patrick and Margaret (née McKenna) Hughes. In reference to the anti-Catholic penal laws of Ireland, he later observed that, prior to his baptism, he had lived the first five days of his life on terms of "social and civil equality with the most favored subjects of the British Empire." He and his family suffered religious persecution in their native land; his late sister was denied a Catholic burial conducted by a priest, and Hughes himself was nearly attacked by a group of Orangemen when he was about fifteen. He was sent with his elder brothers to a day school in the nearby village of Augher, and afterwards attended a grammar school in Aughnacloy.
Patrick Hughes, a poor but respectable tenant farmer, was forced to withdraw John from school and sent him to work one of his farms. However, being disinclined to farm life, he was placed as an apprentice to Roger Toland, the gardener at Favour Royal Manor, to study horticulture. His family emigrated to the United States in 1816 and settled in Chambersburg, Pennsylvania. Hughes joined them there the following year. He made several unsuccessful applications to Mount St. Mary's College in Emmitsburg, Maryland, where he was eventually hired by its Rector, the Abbé John Dubois, S.S., as a gardener. During this time he befriended Mother Elizabeth Ann Seton, who was favorably impressed by Hughes and persuaded Dubois to reconsider his admission. Hughes was subsequently admitted as a regular student of Mount St. Mary's in September 1820. In addition to his studies, he continued to supervise the garden, and served as a tutor in Latin and mathematics, as well as prefect over the other students.
Present day descendants of John Hughes include Peter Hughes, Ethnea Ferguson, and Patricia Donnelly. Peter Hughes' family expands to his daughter Aimee Lilly and her five children Griffin, Allison, Gavin, Garran, and Gillon Lilly. Patrick Hughes and his two children Lola and Balen Hughes, and his other son Peter John Hughes and his son Jonathon Hughes. Patricia Donnelly's family expands to her daughters Colleen and Patti-Lynn and her son Ted. She has five grandchildren named, David, Connor, Kylie, Gavin, and Dylan. Ethnea Ferguson's family expands to her daughter Erin and son Blake and her grandchild Oscar.
As a seminarian, Hughes resolved to serve his home Diocese of Philadelphia, then governed by Bishop Henry Conwell. The bishop, while performing a canonical visitation of his diocese, met Hughes at his parents' home in Chambersburg and invited him to accompany him on the remainder of his visitation. On October 15, 1826, Hughes was ordained to the priesthood by Bishop Conwell at St. Joseph's Church in Philadelphia.
Hughes' first assignment was as a curate at St. Augustine's Church in Philadelphia, where he assisted its pastor, the Rev. Father Michael Hurley, O.E.S.A., by celebrating Mass, hearing confessions, preaching sermons, and other duties in the parish. Later that year he was sent to serve as a missionary in Bedford, where he secured the conversions of several Protestants. In January 1827, he was recalled to Philadelphia and named pastor of St. Joseph's Church. He laboured afterwards at St. Mary's Church, whose trustees were in open revolt against the bishop, and were subdued by Hughes only when he built St. John the Evangelist Church in 1832, then considered one of the finest in the country. Previous to this, in 1829, he founded St. John's Orphan Asylum.
About this time Hughes became engaged in a public controversy over Catholic beliefs with the Rev. John A. Breckinridge, a distinguished Presbyterian clergyman and son of the former Attorney General in the Jefferson Administration. Several debates ensued between the two concerning whether Catholicism was compatible with American republicanism and liberty. Though it was predicted that the Irish immigrant would be outclassed by his better educated Protestant adversary, Hughes acquitted himself very well against his opponent's attacks on his religion. The debates resulted in the pugnacious Hughes' emergence as a vigorous defender of Catholicism in America. His name was mentioned for the vacant see of Cincinnati and as a coadjutor for Philadelphia.
Hughes was chosen by Pope Gregory XVI as the coadjutor bishop of the Diocese of New York on August 7, 1837. He was consecrated bishop at St. Patrick's Old Cathedral on January 7, 1838 with the title of the titular see of Basilinopolis, by the Bishop of New York, John Dubois, S.S., his former Rector. Although wishing Hughes no ill, many of the priests in the diocese had favored the popular Rev John Power, Vicar-General. Power had been overlooked for the position in 1826 when Dubois won the appointment as bishop. The clergy demonstrated their disappointment by not attending the consecration.
One challenge Hughes took on upon arriving in New York was the dispute between the trustees of various parishes in the city, who held the control of these institutions. This practice was known as trusteeism, and the bishop challenged both the practicality and the legitimacy of it. Hughes drew upon his experience with this situation in Philadelphia and was able to get a referendum passed by the Catholics of the city in 1841 supporting the authority of the bishop.
Hughes also campaigned actively on behalf of Irish immigrants, and attempted to secure state support for parochial schools. He protested against the standard use of the King James Bible in public schools by the Public School Society, a private organization which operated the schools of New York City. He claimed that it was an attack on Catholic constitutional rights of double taxation, because Catholics would need to pay taxes for public school and also pay for the private school to send their children, to avoid having their children indoctrinated by teachers following the Protestant teachings footnoted in that translation of the Bible. When he failed to secure state support, he founded an independent Catholic school system which became an integral part of the Catholic Church's structure at the Third Plenary Council of Baltimore (1884), which mandated that all parishes have a school and that all Catholic children be sent to those schools.
Hughes was appointed Apostolic Administrator of the diocese the following year, due to Dubois' failing health. As coadjutor, he automatically succeeded Dubois upon the bishop's death on December 20, 1842. He took over a diocese which covered the entire State of New York and northern New Jersey, having only some 40 priests to serve a Catholic population estimated to be about 200,000 at the time.
In 1844 anti-Catholic riots instigated by Nativist agitators threatened to spread to New York from Philadelphia, where two churches had been burned and twelve people had died. Hughes put armed guards at Catholic churches and famously told the Nativist sympathizing mayor that "if a single Catholic Church were burned in New York, the city would become a second Moscow" - a reference to the Russian scorched earth policy before Napoleon's arrival. City leaders took him at his word, and the anti-Catholic faction was not allowed to conduct its rally.
Hughes founded the Ultramontane newspaper the New York Freeman to express his ideas. In 1850 he delivered an address entitled "The Decline of Protestantism and Its Causes," in which he announced as the ambition of Catholicism "to convert all Pagan nations, and all Protestant nations . . . Our mission [is] to convert the world—including the inhabitants of the United States—the people of the cities, and the people of the country . . . the Legislatures, the Senate, the Cabinet, the President, and all!"
Hughes held a "strong commitment to the cause of Irish freedom" but also felt that immigrants, particularly his fellow Irish immigrants, "should demonstrate their unswerving loyalty to their adopted land."
Hughes became an archbishop on July 19, 1850, when the diocese was elevated to the status of archdiocese by Pope Pius IX. As archbishop, Hughes became the metropolitan for the Catholic bishops serving all the dioceses established in the entire Northeastern United States. He convened the first meeting of the Ecclesiastical Province of New York in September 1854. After this he traveled to Rome, where he was present at the proclamation of the Immaculate Conception as a dogma of the Catholic Church by Pope Pius. Hughes served as President Lincoln's semiofficial envoy to the Vatican and to France in later 1861 and early 1862. Lincoln also sought Hughes' advice on the appointment of hospital chaplains.
In an address in March 1852, Hughes lionized what he referred to the the "spirit of the constitution," expressed hope that the "parties" of the republic would be completely "penetrated" by that spirit, and stated that the founders' achievements in the realm of religious freedom were "original" in history and that the constitution's "negation of all power to legislate" on "rights of conscience" made American law on that topic superior to that of other countries which had secured these rights "by some positive statue." In the same address, Hughes also expressed sentiments of religious toleration, stating that "we are indebted" to the "liberality of Protestantism" with respect to the worldviews of the framers of the Constitution who, in his words, "were almost, if not altogether, exclusively Protestants," while averring that the strong leadership of Washington and the variety of opposing Protestant views were likely more influential to the framers' stance on religious freedom than Protestantism itself. Hughes also stated that "the great men who framed the Constitution saw, with keen and delicate perception, that the right to tolerate implied the equal right to refuse toleration, and on behalf of the United States, as a civil government, they denied all right to legislate in the premises, one way or the other." He affirmed the role of Catholic soldiers in American wars, declaring "I think I shall be safe in saying that there has not been one important campaign or engagement in which Catholics have not bivouacked, fought, and fallen by the side of Protestants, in maintaining the rights and honor of their common country." Hughes also said that "It is...out of place, and altogether untrue, to assert or assume that this is a Protestant county or a Catholic country. It is neither. It is a land of religious freedom and equality; and I hope that, in this respect, it shall remain just what it now is to the latest posterity," and also that "Catholics, as such, are by no means strangers and foreigners in this land...The Catholics have been here from the earliest dawn of the morning."
Hughes held misgivings regarding slavery, but felt that the conditions of the "starving laborers" in the Northern states were often worse than that of slaves in the South, and also believed that the abolitionist movement could veer towards ideological excess. He felt that abolitionists were wrong when they focused on the hardships of Southern slaves while disregarding the issues facing Northern urban workers.
Hughes served as archbishop until his death. He was originally buried in old St. Patrick's Cathedral, but his remains were exhumed in 1882 and reinterred in the crypt under the altar of the new St. Patrick's Cathedral which he had undertaken to build.
Hughes has been described as "impetuous and authoritarian, a poor administrator and worse financial manager, indifferent to the non-Irish members of his flock, and prone to invent reality when it suited the purposes of his rhetoric."
Historian Daniel Walker Howe is more laudatory, suggesting that Hughes "labored to bring a largely working-class Irish community into a meaningful relationship with Catholic Christianity" while at the same time working "to conciliate middle-class Catholics and Protestant well-wishers whose financial support he needed for his amazingly ambitious program of building." Howe continues, "Although no theologian, John Hughes ranks high for political judgment and in the significance of his accomplishments among nineteenth century American statesmen, civil as well as ecclesiastical. He successfully coped with fierce party competition in New York, bitter battles over the public school system, revolutions in Europe, the rise of nativism across the United States, and soaring rates of immigration after the Irish Potato Famine. He encouraged his people to hard work, personal discipline, and upward social mobility." "Crucially, he combined his staunch American patriotism with staunch devotion to a nineteenth-century papacy deeply suspicious of all liberalism, especially American." Hughes "succeeded in fostering a strong Irish American identity, one centered on the Catholic faith rather than on the secular radicalism of the Irish nationalists who competed with him for community leadership." This achievement, however, came "at the cost of losing to the Irish-American community the Irish Protestant immigrants."
According to his later successor, Patrick Cardinal Hayes, named archbishop of New York in 1919, Archbishop Hughes was severe of manner, and kindly of heart, but was not aggressive until assailed.
In New York, Hughes founded St. John's College (now Fordham University) and, under his administration, invited many religious congregations to staff schools in New York, among them members of the Society of Jesus, to whom he entrusted the care of his college, who also established Fordham Prep; the Brothers of the Christian Schools who founded Manhattan College; and established as an autonomous congregation the Sisters of Charity of New York, who founded the Academy of Mount St. Vincent (now College of Mount Saint Vincent).
To the dismay of many in New York's Protestant upper-class, Hughes foresaw the uptown expansion of the city and began construction of the current St. Patrick's Cathedral on Fifth Avenue between 50th and 51st Street, laying its cornerstone on August 15, 1858. It was not completed until after his death. At the time, due to its remote location in a still-rural part of Manhattan, the new cathedral was initially dubbed "Hughes' Folly" by the press for many years. Ultimately, Hughes' foresight proved providential, as the rapid urban growth uptown would soon place the new cathedral in the emerging urban center of midtown Manhattan.