Buwad, during the late 18th century, Spain had territorial holdings in Formosa as well as in some parts of India as well as had claims in the Mollacas (Spice Islands; Malaya) as during this time parts of the Mollacas was under Portuguese control, and Spain at this time considered Portugal as an 'independent' province of the Empire.
I refuse to accept the fact that the Spanish, who all to eradicated the Aztecs and the Incans (whose populations were in the tens of millions and who had a far more advanced civilization than the Malays) would have been impeded by muslims in the south. And I doubt it would have been too difficult since the population in Mindanao during this time, as documented by Spanish episcopacy was not even in the millions, but in the hundreds of thousands.
The reason for a greater Moro resistance was the fact that Spain, during the late 18th century was in the verge of an monarchical change, King Charles IV, Emperor of the Spanish Empire from 1788 till 1808 adopted a political regimen called Pax Hispanicana Abstantes, which focused more on diplomatic peace and conservancy. Spain, at this time, reached its zenith in power; with control of almost all of North America (albeit the lower half), all of central America, all of South America (aside from Portuguese controlled Brasilia; though Spain considered Portugal and its possessions as part of the Paternal Spanish Empire by right of power), possessions in Africa, territorial rights in India and claims in the pacific, including the Royal Colony of Las Islas de Felipe. The Empire controlled the largest land forces in the entire world at the time, with the rival of the French; the Empire's Navy was unprecedented, and would not be ecclipsed for another quarter of a century by the British.
It was Charles IV's adopting of a conservancy tactic that led to the demise of the Envanglism in Mindanao; as his predecessor, Emperor Ferdinand VI had implemented decades before. Ferdinand VI was one who was as imperialistic and militant in expansion as that his ancestor, Philip II the Great (who our country was named after).
Had the Spaniards continued militant christian evangelism in the south; even as to strategically conquor Borneo and extend its christian evangelism in that island, this problem we have of militant islam wouldn't even have manifested.
It was Spanish Christian Evangelism that converted Luzon, which was Muslim may I add, to a Christian island. And it was Spanish Christian Evangelism that propelled the Visayas (Bohol Included) into a Christian seat.
The Only reason why Mindanao remains the way it is (a large muslim presence) was because of the change of policies enacted by King Charles IV.
Suffice to say, I do not believe that a group of Muslim misfits were able to stave back the might of the Spanish Empire, which quite frankly feared no military force in this earth for almost 3-4 centuries.
The following are the Spanish Monarchs that I discussed above:
Emperor Ferdinand VI, Emperor of the Spanish Empire. Of the Bourbon Dynasty.
This man was a militant Emperor and pursued active conquest. His diplomatic skill was similar to his ancestor, Philipp II the Great. He was raised during the late mid-late 17th century under the notion of Monarchical Absolutism; that the power of the King of Spain came directly from GOD himself.
King Charles IV of Spain. A far more 'laxed' monarch as compared to his predecessors. Charles IV was educated under the notion of European Enlightenment and the concept of Universalism, Fraternity, Egalitarianism. Far less militant as his predecessors, I dare say. His policies manifested this in the Philippines.
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