January – In Russia, it is the beginning of the Oprichnina under Ivan the Terrible.
January 26 – The Battle of Talikota, a watershed battle fought between the Vijayanagara Empire and the Deccan sultanates, greatly weakens the last Hindu kingdom in South India.
February 13 – Spanish Conquistador Miguel López de Legazpi lands with his troops on the shores of Cebu Island in the Philippines.
March 1 – The city of Rio de Janeiro, Brazil, is founded as São Sebastião do Rio de Janeiro by the Portuguese.
April 27 – Cebu City is established as San Miguel by López de Legazpi, becoming the first Spanish settlement in the Philippines.
May 18 – Ottoman troops land on the island of Malta, beginning the Siege of Malta.
June 17 – Matsunaga Hisahide assassinates the 13th Ashikaga shogun, Ashikaga Yoshiteru.
July 29 – Mary, Queen of Scots, widowed, marries Henry Stuart, Lord Darnley.
August 6 – Sark granted as a Fief by Elizabeth I to Hellier de Carteret Seigneur of Saint Ouen
August 28 – St. Augustine, Florida (named after St. Augustine), is established. It is the oldest remaining European settlement in the United States.
September 4 – The Spanish fleet of Pedro Menéndez de Avilés lands on modern-day Florida to oust the French under Jean Ribault. He later destroys the French colony of Fort Caroline.
September 8 – Pedro Menéndez de Avilés settles in St. Augustine, Florida.
September 11 – The Knights of Malta lift the Siege of Malta after four months.
October – The first Martello tower, the Tour de Mortella, designed by Giovan Giacomo Paleari Fratino (el Fratin), is completed as part of the Genovese defence system at Mortella (Myrtle) Point in Upper Corsica.
October 18 – Ships belonging to the Matsura clan of Japan fail to capture the Portuguese trading carrack in the Battle of Fukuda Bay, the first recorded naval battle between Japan and the West.
The pencil is first documented by Conrad Gesner; it is becoming common in England.
John Beddoes School is founded at Presteigne in Wales.
Huntingdon Grammar School is established.
January 17 – Mariana Navarro de Guevarra Romero, Spanish Roman Catholic nun, member of the Mercedarian Tertiaries (d. 1624)
February 13 – Willem Baudartius, Dutch theologian (d. 1640)
March 23 – Eilhard Lubinus, German theologian (d. 1621)
April 2 – Cornelis de Houtman, Dutch explorer (d. 1599)
April 3 – Anna III, Abbess of Quedlinburg (d. 1601)
May 15 – Hendrick de Keyser, Dutch sculptor and architect born in Utrecht (d. 1621)
June 2 – Francisco Ribalta (d. 1628)
July 6 – Hugh Hamersley, Lord Mayor of London, 1627–1628 (d. 1636)
August 5 - Paola Massarenghi, Italian composer (d. unknown)
August 9 – Louis II, Count of Nassau-Weilburg (d. 1627)
August 16 – Christina, Grand Duchess of Tuscany (d. 1637)
August 29 – Agostino Ciampelli, Italian painter (d. 1630)
September 17 – Edward Fortunatus, German nobleman (d. 1600)
September 28 – Alessandro Tassoni, Italian poet and writer (d. 1635)
October 6 – Marie de Gournay, French writer (d. 1645)
October 12 – Ippolito Galantini, Founder of the Congregation of Christian Doctrine of Florence (d. 1619)
October 22 – Benedikt Carpzov the elder, German legal scholar (d. 1624)
Robert Devereux, 2nd Earl of Essex, English nobleman and politician (d. 1601)
Laurentius Paulinus Gothus, Swedish theologian and astronomer (d. 1646)
November 14 – Petrus Bertius, Flemish theologian and scientist (d. 1629)
December 2 – Toby Caulfeild, 1st Baron Caulfeild, Northern Irish politician (d. 1627)
Reza Abbasi, Persian painter and calligrapher (d. 1635)
Ferdinando Gorges, English colonial entrepreneur (d. 1647)
John Davies of Hereford, Welsh poet (d. 1618)
Francis Meres, English churchman and author (d. 1647)
Pedro Fernandes de Queirós, Portuguese seaman and explorer (d. 1614)
John Spottiswoode, Archbishop of St. Andrews (d. 1639)
Francis Tanfield, Governor of the South Falkland colony
Edmund Whitelocke, English soldier and courtier (d. 1608)
Robert Wintour, English conspirator (d. 1606)
Maria Pita, Spanish heroine (d. 1643)
Gregor Aichinger, German composer (d. 1628)
George Kirbye, English composer (d. 1634)
Duarte Lobo, Portuguese composer (d. 1646)
January 19 – Diego Laynez, Spanish Jesuit theologian (b. 1512)
March 17 – Alexander Ales, Scottish theologian (b. 1500)
c. late March? – Lope de Rueda, Spanish dramatist (b. c. 1510)
May 14 – Nicolaus von Amsdorf, German Protestant reformer (b. 1483)
May 28 – Mikołaj "the Black" Radziwiłł, Polish magnate (b. 1515)
June 12 – Adrianus Turnebus, French classical scholar (b. 1512)
June 17 – Ashikaga Yoshiteru, Japanese shogun (b. 1536)
August – Jacques Buus, Flemish composer and organist (b. 1500)
June 25 – Herluf Trolle, Danish Admiral of Fleet and co-founder of Herlufsholm School (b. 1516)
September 13 – William Farel, French evangelist (b. 1489)
September 20 – Cipriano de Rore, Flemish composer and teacher (b. 1515)
October 4 – Pier Paolo Vergerio, Italian reformer (b. 1498)
October 5 – Lodovico Ferrari, Italian mathematician (b. 1522)
October 12 – Jean Ribault, French explorer and colonizer (b. 1520)
October 14 – Thomas Chaloner, English statesman and poet (b. 1521)
October 22 – Jean, Vicomte d'Aguisy Grolier de Servieres, French bibliophile (b. 1479)
November 25 – Hu Zongxian, Chinese general (b. 1512)
December 9 – Pope Pius IV (b. 1499)
December 13 – Conrad Gessner, Swiss naturalist (b. 1516)
Antonio Bernieri, Italian painter of the Renaissance period (b. 1516)
Kat Ashley, governess of Elizabeth I of England
Yadegar Mokhammad of Kazan, last khan of Kazan Khanate
Paweł Tarło, canon of Kraków
Year 1565 (MDLXV) was a common year starting on Monday (link will display the full calendar) of the Julian calendar.