The family Iguanodectidae comprises small characiform fishes widely distributed across the Amazon Basin, yet species boundaries within some taxa remain poorly understood. In this study, we analyzed specimens of Iguanodectes purusi, collected from the Purus River, and I. spilurus, from different localities including the Madeira River (Aveiro). Phylogenetic analyses based on molecular markers recovered I. purusi nested within the I. spilurus (sensu stricto) clade, with extremely low genetic divergence between them (0.005 ± 0.005). Morphological analyses revealed strong similarities between the two taxa, including a complete lateral line with 60–64 perforated scales, eight scales between the lateral line and the dorsal-fin origin, five scales between the lateral line and the pelvic fin, and an anal fin with 32–34 branched rays. General coloration is light, with a silvery stripe along the midline of the body and a dark blotch on the upper caudal-fin lobe. I. spilurus is the only species of the genus recorded in the main channel of the Madeira River, whereas the other congeners were found exclusively in terra firme streams. Despite these similarities, I. purusi exhibits subtle differences, such as a higher number of predorsal scales (≥27 in I. purusi vs. ≤26 in I. spilurus) and more perforated scales on the lateral line (>65 in I. purusi vs. 60–64 in I. spilurus). However, these differences may represent geographic (clinal) variation among populations distributed across the Amazon Basin rather than valid species-level differentiation. Our findings highlight the need for taxonomic revisions integrating molecular, morphological, and ecological data to clarify the status of I. purusi and to better understand diversity patterns within Iguanodectidae.