When the Spaniards began colonizing the Philippines, they saw an already-developed weapons-based martial arts practiced by the natives.
After the decree prohibiting the native to carry full-sized swords (such as the Kris and the Kampilan), the elite and underground practitioners maintained and kept the art alive. To circumvent the decree, some practitioners used sticks made out of rattan rather than swords, as well as small knives wielded like a sword. Eskrima can be traced back from the Portuguese Tomé Pires' Suma Oriental to Lapu-lapu.
As eskrima is an art for the common folk (as opposed to nobility or warrior classes), most practitioners lacked the scholarly education to create any kind of written record. While the same can be said of many martial arts, this is especially true for eskrima because almost all of its history is anecdotal, oral or promotional. The origin of eskrima can be traced back to the fighting systems used by Filipinos during internal conflicts. Settlers and traders travelling through the Malay Archipelago brought the influence of silat as well as Chinese and Indian martial arts. Some of the population still practices localised Chinese fighting methods known as kuntaw.
Among the earliest written records of Filipino martial arts comes from the Spanish conquistadors who fought native tribesmen armed with sticks and knives. Driven back to their ships, the European colonists had to resort to fire-arms to defeat the Filipinos. In 1521, Ferdinand Magellan was killed in Cebu at the Battle of Mactan by the forces of Raja Lapu-Lapu, the Mactan tribal chief. Although eskrimadors hold that Lapu-Lapu killed Magellan in a sword-fight, the only eyewitness account of the battle by chronicler Antonio Pigafetta tells that he was stabbed in the face and the arm with spears and overwhelmed with multiple warriors who hacked and stabbed at him:
The natives continued to pursue us, and picking up the same spear four or six times, hurled it at us again and again. Recognizing the captain, so many turned upon him that they knocked his helmet off his head twice, but he always stood firmly like a good knight, together with some others. Thus did we fight for more than one hour, refusing to retire farther. An Indian hurled a bamboo spear into the captain's face, but the latter immediately killed him with his lance, which he left in the Indian's body. Then, trying to lay hand on sword, he could draw it out but halfway, because he had been wounded in the arm with a bamboo spear. When the natives saw that, they all hurled themselves upon him. One of them wounded him on the left leg with a large cutlass, which resembles a scimitar, only being larger. That caused the captain to fall face downward, when immediately they rushed upon him with iron and bamboo spears and with their cutlasses, until they killed our mirror, our light, our comfort, and our true guide. When they wounded him, he turned back many times to see whether we were all in the boats. Thereupon, beholding him dead, we, wounded, retreated, as best we could, to the boats, which were already pulling off.
Spanish was the lingua franca of the Philippines until the early 20th century. Some theorize that there were groups of conquistadors and Jesuit warrior-priests who taught the Indios how to defend themselves against Moro raiders. Saint Ignatius of Loyola, the founder of the Jesuit order was a veteran knight and soldier and many Jesuits knew how to defend themselves as they were generally dispatched into the most dangerous areas by the Pope. One of the apparent influences from Spanish styles is the espada y daga (sword and dagger) method, but some disagree as Filipino espada y daga appears to be distinct from European rapier and dagger techniques; the stances are different as weapons used in Eskrima are typically shorter than European swords.
One thing that is known is that some of the arts were hidden from the Spaniards and passed down through familial or communal ties, usually practiced under the moonlight or right under the Spaniards noses by disguising them as entertainment like with choreographed dances such as the Sakuting stick dance (see Youtube videos) or during mock battles at Moro-moro (Moros y Cristianos) stage plays. Due to the way the arts were then clandestinely practiced, one apparent effect of Spanish subjugation and disarmament of the civilian population was the evolution of unique and complex stick-based techniques in the Visayas and Luzon regions (unlike Southern Mindanao which retains almost exclusively blade-oriented techniques as it was never fully conquered and disarmed by the Spaniards and Americans)
Although the turbulent and conflict-fraught history and environment of the Philippines enabled eskrima to develop into an efficient art, this has changed in the sense that some systematization allowed easier and quicker teaching of the basics. With the exception of a few older and more established systems, it was previously common to pass the art from generation to generation in an informal approach. This has made attempts to trace the lineage of a practitioner difficult. For example, Antonio Illustrisimo seemed to have learned to fight while sailing around the Philippines, while his nephew and student Floro Villabrille claimed to have been taught by a blind Moro princess in the mountains – a claim later refuted by the older Illustrisimo. Both have since died.