Since the disintegration of the Great Colombia, the Isthmus fought for its independence with little success until 1903. The separation of Panama from Colombia was formalized on 3 November 1903, with the establishment of the Republic of Panama. Due to the jungles and lack of development and the proper means of transportation and communications, the news that "Gran Colombia" had disintegrated did not reach Panama soon enough, causing the Isthmus to end up attached to the then formed, Republic of Colombia.
After its independence from Spain on November 28, 1821, modern-day Panama became a part of the Republic of Gran Colombia which consisted of today's Colombia, Venezuela, Panama, and Ecuador.
The political struggle between federalists and centralists that followed independence from Spain resulted in a changing administrative and jurisdictional status for Panama. Under centralism Panama was established as the Department of the Isthmus and during federalism as the Sovereign State of Panama.
In 1846 a treaty between Colombia and the United States was signed. In the treaty the United States was obliged to maintain "neutrality" in Panama in exchange for transit rights in the isthmus on behalf of Colombia. In March 1885 Colombia thinned its military presence in Panama by sending troops stationed there to fight rebels in other provinces. These favourable conditions prompted an insurgency in Panama. The United States Navy was sent there to keep order, in spite of invoking its obligations according to the treaty being signed in 1846.
In 1885 the United States occupied the city of Colón, Panama. Chile, which had by the time the strongest fleet in the Americas, sent the cruiser Esmeralda to occupy Panama City in response. Esmeralda's captain was ordered to stop by any means an eventual annexation of Panama by the United States.
The Thousand Days' War (1899–1902) was one of the many armed struggles between the Liberal and Conservative Parties which devastated Colombia, including Panama, during the 19th century. This last civil war ended with the signing of the Treaty of Wisconsin. However, the Liberal leader Victoriano Lorenzo refused to accept the terms of the agreement and was executed on May 15, 1903.
On July 25, 1903, the headquarters of the Panamanian newspaper El Lápiz were assaulted by orders of the military commander for Panama, General José Vásquez Cobo, brother of the then Colombian Minister of War, as a retaliation for the publication of a detailed article narrating the execution and protests in Panama. This event damaged the trust of Panamanian liberals in the Conservative government based in Bogotá, and they later joined the separatist movement.
In 1903, the United States and Colombia signed the Hay–Herrán Treaty to finalize the construction of the Panama Canal but the process was not achieved because the Congress of Colombia rejected the measure (which the Colombian government had proposed) on August 12, 1903. The United States then moved to support the separatist movement in Panama to gain control over the remnants of the French attempt at building a canal.
Panamanian politician José Domingo De Obaldía was selected to become the Governor of the Isthmus of Panama office that he had previously held and was supported by the separatist movements. Another Panamanian politician named José Agustín Arango began to plan the revolution and separation. The separatists wanted to negotiate the construction of the Panama canal directly with the United States due to the negativity of the Colombian government.
The separatist network was formed by Arango, Dr. Manuel Amador Guerrero, General Nicanor de Obarrio, Ricardo Arias, Federico Boyd, Carlos Constantino Arosemena, Tomás Arias, Manuel Espinosa Batista and others. Manuel Amador Guerrero was in charge of traveling to the United States to get support for the separatist plan; he also gained the support of important Panamanian liberal leaders and the support of another military commander, Esteban Huertas.
With a strong support the separatist movement set November 1903 as the time for the separation. However, rumors in Colombia spread but the information managed by the government of Colombia indicated that Nicaragua was planning to invade a region of northern Panama known as the Calovébora. The Government deployed troops from the Tiradores Battalion from Barranquilla, and instructed the commander to take over the functions of the Governor of Panama José Domingo de Obaldía and General Esteban Huertas, who were not trusted by the government.
The Tiradores Battalion was led by Generals Juan Tovar and Ramón Amaya and arrived in the Panamanian city of Colón in the morning of November 3, 1903. The battalion suffered delays on its way to Panama City caused by the complicity of the Panama Railway authorities who sympathized with the separatist movement. Upon arrival in Panama City, the troops were put under the command of Col. Eliseo Torres. General Esteban Huertas commander of the Colombia Battalion in Panama ordered the arrest of Tovar and his other officials.
The Colombian gunboat Bogotá fired shells upon Panama City the night of November 3 causing injuries and mortally wounding Mr. Wong Kong Yee of Hong Sang, China.
A United States Navy gunboat, USS Nashville, commanded by Commander John Hubbard, who had also helped to delay the disembarkation of the Colombian troops in Colón, continued to interfere with their mission by alleging that the "neutrality" of the railway had to be respected.
With the suppression of the Colombian troops, the Revolutionary Junta proceeded to declare the separation of the Isthmus and later the independence with the declaration of the Republic of Panama. A naval squadron in the Bay of Panama was captured without resistance. Demetrio H. Brid the president of the Municipal Council of Panama became the de facto President of Panama appointing on November 4, 1903 a Provisional Government Junta that governed the country until February 1904 when the Constituent National Convention was established and elected Manuel Amador Guerrero as first constitutional president. News of the separation of Panama from Colombia reached Bogotá on November 6, 1903 due to a problem with the submarine cables.
On November 13, 1903 the United States formally recognized the Republic of Panama (after recognizing it unofficially on November 6 and 7). On November 18, 1903 the United States Secretary of State John Hay and Philippe-Jean Bunau-Varilla signed the Hay–Bunau-Varilla Treaty. No Panamanians signed the treaty although Bunau-Varilla was present as the diplomatic representative of Panama (a role he had purchased through financial assistance to the rebels), despite the fact he had not lived in Panama for seventeen years before the incident, and he never returned. The treaty was later approved by the Panamanian government and the Senate of the United States.
The ambassador of Colombia in Ecuador Emiliano Isaza was informed of the situation in Panama but did not inform his government to prevent a revolt in Bogotá. The government of Colombia then sent a diplomatic mission to Panama in an effort to make them reconsider by suggesting an approval by the senate of Colombia if they reconsidered the Hay–Herrán Treaty instead of the Hay–Bunau-Varilla Treaty and also proposed making Panama City the capital of Colombia.
The mission met aboard the ship USS Mayflower with the Panamanian delegation formed by Constantino Arosemena, Tomás Arias and Eusebio A. Morales, which rejected all proposals. Colombia then sent later a delegation of prominent politicians and political figures; General Rafael Reyes, Pedro Nel Ospina, Jorge Holguín and Lucas Caballero who met with the same representative for Panama and Carlos Antonio Mendoza, Nicanor de Obarrio y Antonio Zubieta, without reaching any consensus.