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The aim of the present study was to perform comparative histological analyses of the ontogenetic development of two fish species endemic to the Sao Francisco River in Brazil: Prochilodus argenteus and Lophiosilurus alexandri. Histological analyses were performed every 24 h from the moment of hatching until 14 days post-hatching (dph) for the observation of larval development and until 39 dph for the observation of gonadal development. Whole larvae were fixed in Bouin's solution and the histological slides were stained with haematoxylin-eosin. Lophiosilurus alexandri larvae had a larger body size compared with P. argenteus larvae since hatching. Lophiosilurus alexandri larvae had mouth opening and pigmentation of the eyes upon hatching, whereas these events were observed at 1 dph in P. argenteus larvae. The visualisation and the inflation of the swim bladder occurred at 1 and 3 dph, respectively, in the P. argenteus, whereas these events occurred at 2 and 8 dph, respectively, in L. alexandri. Yolk granules were absorbed at 4 dph in P. argenteus and the 10 dph in L. alexandri. At 7 dph, the digestive tube was more differentiated in L. alexandri than P. argenteus and at 14 dph, the digestive system of both species had features of their eating habits: broad stomach and short intestine in L. alexandri, typical of carnivorous habits; stomach with a mechanical function and long intestine in P. argenteus, typical of detritivorous habits. The epithelial lining tissue, formed by a single layer of cells in the newly hatched larvae (0 dph), differentiated throughout the study, exhibiting scales in P. argenteus and numerous club cells in the middle epithelial region of L. alexandri at 39 dph. Undifferentiated gonads with somatic cells and primordial germ cells were observed at 39 dph, with caudal-cranial migration since 1 dph in both species. The anatomic changes during the ontogeny of P. argenteus and L. alexandri larvae are directly associated with the evolutionary history of each species, which explains their feeding habits, behaviour and distribution in the environment: Prochilodus argenteus is detritivorous and actively swims in the water column, whereas L. alexandri is carnivorous and inhabits bottom regions. At 39 dph neither species exhibited sexual differentiation.