Resource partitioning is considered one of the main processes driving diversification in ecological communities because it allows coexistence among closely related and ecologically equivalent species. We combined three complementary approaches, i.e. the evaluation of foraging behaviour, diet composition and nutritional condition (RNA:DNA ratio), to assess feeding by two closely related (sister) butterflyfishes that are syntopic in Puerto Rico. Chaetodon capistratus had a higher abundance and higher bite rate and selected octocorals and hard corals for feeding, whereas Chaetodon striatus fed preferentially on sandy substrates. Cnidarians and polychaetes were the most representative diet items for both species, but C. capistratus preferred the former (Feeding Index of 74.3%) and C. striatus the latter (Feeding Index of 60.4%). Similar RNA:DNA ratios for both species suggest that, although they differ in feeding rates and diet, C. capistratus and C. striatus have similar nutritional fitness. Therefore, these species are both zoobenthivores but show clear differences in their substrate selection. The differences in the use of foraging substrate by C. capistratus and C. striatus, despite their close phylogenetic relationship and similar diets, suggest that these species coexist by resource partitioning.