Understanding “why species are where they are” at different scales is one of the main focuses of ecological and biogeographical studies. Although ecological features, such as trophic group and species abundance, are thought to be more important for driving co-occurrence patterns at the habitat scale, it is not yet known if phylogenetic constraints can also exert some influence. Here, we studied global co-occurrence patterns of butterflyfishes in relation to species abundance, trophic characteristics, and evolutionary histories, specifically examining two questions—Question (1): does phylogenetic affinity and/or abundance explain co-occurrence at the habitat scale? To answer this, we used abundance data from 23 global localities to evaluate whether phylogenetic affinity alone as well as after accounting for differences in diet among sympatric species explains co-occurrences at the habitat scale. Question (2): are the diets of sister species from the Atlantic Ocean and the Eastern Pacific phylogenetically conserved? To examine this, we used a more detailed diet classification of species present within these realms. We found that phylogenetic distance per se fails to explain the co-occurrence of butterflyfish species pairs. Instead, species abundance exerted a major influence on interspecific co-occurrences. We also found no correlation between phylogenetic distance and diet similarities for Atlantic and East Pacific butterflyfishes; thus, in these regions, species' diets do not seem to be phylogenetically conserved. This suggests that evolutionary processes are not the main drivers of butterflyfish co-occurrence highlighting species' abundance and niche-related processes as the most important factors in determining whether species co-occur at the habitat scale.