The term Moro, as used to describe Islamic Filipinos from the Southern Islands of the Philippine Archipelago, is Spanish meaning simply 'Moor.'
The Moors, the primary historical grouping that was primarily Berber North African, had conquered the majority of Spain in the Seventh Century A.D. and were only ejected from their Southern strongholds in the year 1492 by a unified Spain. When Islamic Filipinos were encountered by Spanish explorers, therefore, it made perfect sense to them that these new Islamic enemies also be called Moors. Remember, these are the same folks who started calling Native Americans 'Indians,' despite some evidence to the contrary.
I have seen some online accounts that insist on using the laborious term 'Islamic Filipino' instead of the more colloquial term 'Moros.' However, since they tend to self identify as Moros, it seems appropriate to use the more familiar term. In fact, a modern organization called the Moro Islamic Liberation Front (or MILF, but just try looking that up on Google :) is the continuation, if you will, of the rebellion against any rule except by Islamic factions. If they use it, it must be the correct term, right? I will continue use of the term, if only to save keystrokes on my overworked digits.