The Dagohoy Rebellion was one of two significant revolts that occurred in Bohol, Philippines during the Spanish Era. The other one was the Tamblot Uprising in 1621 led by Tamblot, a babaylan or native priest from Bohol which was basically a religious conflict
Unlike the Tamblot revolt, the Dagohoy rebellion was not a religious conflict. Rather, it was like most of the early revolts which were ignited by forced labor, Spanish oppression,bandala, excessive tax collection and payment of tributes. On top of these injustices of the Jesuit priests, what triggered Dagohoy most was the refusal of the Jesuit priest to give a Christian burial to his brother who died in service while chasing a fugitive who went against Christianity. This caused Dagohoy to call upon his fellow Boholanos to raise arms against the oppressors. The rebellion outlasted several Spanish Governor Generals and several missions.
In 1744, Father Gaspar Morales, the Jesuit curate of Inabanga, ordered a constable name Sagarino, to capture a man who had abandoned his Christian religion. The brave constable pursued the fugitive, but the latter resisted and killed him. His corpse was brought to town. Father Morales refused to give the constable Christian burial because he had died in a duel and this was banned by the Church.
Francisco Dagohoy, brother of the deceased Sagarino, became so infuriated at the priest that he instigated the people to rise in arms. The signal of the uprising was the killing of Father Giuseppe Lamberti, Italian Jesuit curate of Jagna on January 24, 1744. Shortly afterwards, Father Morales was killed by Dagohoy. The rebellion rolled over the whole island. Bishop Miguel Lino de Espeleta of Cebu, who exercised ecclesiastical authority over Bohol, tried vainly to mollify the rebellious Boholanos.
Dagohoy defeated the Spanish-Filipino forces sent against him. He established a free government in the mountains, and had 3,000 followers, which subsequently increased to 20,000. The patriots remained unsubdued in their mountains stronghold and, even after Dagohoy's death, continued to defy Spanish power.
The Francisco Dagohoy Cave in the town of Danao was the headquarters of Dagohoy. One of the many crystal-studded passages within Dagohoy's cave has an underwater route leading to dry land, and it is said that every time Spaniards would search the cave, Dagohoy would swim underwater through this passage to hide in the breathing space.  Twenty Spanish governors-general, from Gasper de la Torre (1739–45) to Juan Antonio Martinez (1822–25), tried to quell the rebellion and failed. In 1825, General Mariano Ricafort (1825–30), a kind and able administrator, became governor-general of the Philippines. Upon his order, Alcade-mayor Jose Lazaro Cairo, at the head of 2,200 Filipino-Spanish troops and several batteries, invaded Bohol on May 7, 1827. The brave Boholanos resisted fiercely. Alcalde-mayor Cairo won several engagements, but failed to crush the rebellion. In April 1828, another Spanish expedition under Captain Manuel Sanz landed in Bohol. After more than a year of hard campaign, he finally subdued the patriots. By August 31, 1829, the rebellion had ceased. Governor Ricafort, with chivalric magnanimity, pardoned 19,420 survivors and permitted them to live in new villages at the lowlands. These villages are now the towns of Batuanan, Cabulao, Catigbian, and Vilar.
There is little known information about Francisco Dagohoy ; the only information known is that his real name was Francisco Sendrijas and that he was a native of Inabanga, Bohol. He was a cabeza de barangay, or one of the barangay captains of the town.
About Dagohoy , historians believe that his alias, Francisco Dagohoy, was derived from a belief that he had an amulet (called “agimat” in Tagalog and “dagon” in the Cebuano language) that protected him from being harmed by his enemies. The people believed that he possessed the charm of a gentle wind or “hoyohoy” in the Cebuano language that allowed him to jump from one hill to another and from one side of the river to the other. He was believed to have a clear vision inside dark caves and be invisible whenever and wherever he wants to. The Dagohoy surname was derived from his local alias “Dagon sa hoyohoy.”
According to a local historian, Jes Tirol, the name Dagohoy is a concatenation of the Visayan phrase dagon sa hoyohoy meaning talisman of the breeze.
BUST OF FRANCISCO DAGOHOY
The typical flags of revolt used in the Archipelago were generally red so we can't exclude that the flags used by Francisco Dagohoy and his men were red even if we have no sure evidences.