Seahorses are constantly endangered by harvesting for ornamental trade on the Brazilian coast. Information on the ecology and biology of these fish is essential for their conservation. We analyzed the feeding ecology of the seahorses Hippocampus patagonicus and H. reidi, caught as bycatch, on the coast of the Rio de Janeiro state, Brazil. Their diet was analyzed through analysis of their alimentary canal contents. The specimens of H. patagonicus were obtained as bycatch of shrimp fishing in three regions of the state: southern (Angra–Parati), central (Niteri), and northern (Tamoios-Macaé) regions. Hippocampus reidi specimens were captured in São Gonçalo, inside the Guanabara Bay. We assessed differences in diet composition between sexes for both species, between regions only for H. patagonicus, and seasonal variation only for H. reidi. For this purpose, we analyzed the alimentary canal content of 204 individuals of H. patagonicus and 27 of H. reidi. We found that both species feed mainly on small benthic organisms, like crustaceans of the order Amphipoda. According to the PERMANOVA, no differences between sexes were found in both species. This analysis indicated significant differences in the diet of H. patagonicus between regions and seasonal differences for H. reidi. However, our results were inconclusive regarding this variation due to the high volume of highly digested food content. This study provides essential baseline information on the trophic ecology of the seahorses on the Rio de Janeiro coast, which can help to monitor the population of seahorses on sites where they are constantly threatened by harvesting and trade.