An employer discriminates on the basis of national origin when it makes employment decisions based on a person's ancestry, ethnicity or birthplace, or because of traits closely linked to ethnicity (such as surname, accent, cultural identity, and so on). National origin is prohibited by Title VII and the laws of most states.
Filipinos and Africans may be very similar in physical features, but on the average the Africans have far more of certain observable traits than the Filipinos, and vice versa the Filipinos have far more of certain observable traits that the Africans. What I say here can be said of any two groups of people, however they may be delineated by geography (as this question does) by ethnicity as people identify themselves or others, by cultural traits or language, and so forth.
But the bottom line is, we are all human and have far more in common with each other than with any other species and there are no characteristics that Filipinos have that are not found among the Africans or among any other group of people geographically delineated, or, for that matter, delineated in any other way.