Abstract We reassessed the taxonomic status of lizards of the Iphisa elegans complex, a monotypic genus of Gymnophthalmidae, based on the congruence between mitochondrial DNA (Cytb) and nuclear DNA (c-mos and prlr) and characters of internal and external morphology, both quantitative and qualitative (meristic, morphometric and hemipenial), throughout its wide Amazonian distribution. The congruence of three species delimitation analyses (mPTP, bGMYC and ASAP), nuclear DNA topology and morphological evidence resulted in nine operational taxonomic units in the genus Iphisa. Besides being recovered as monophyletic groups in mitochondrial and nuclear phylogenetic trees, these nine operational taxonomic units can be distinguished by external and hemipenial morphology. Finally, we propose a new taxonomic rearrangement of the genus, whereby we: (i) restrict I. elegans to north-east Amazonia in the Guiana Shield and southwards, west from the Purus–Madeira interfluvium, on the right bank of the Amazon River; (ii) elevate Iphisa elegans soinii Dixon, 1974 to the specific level Iphisa soinii Dixon, 1974 comb. nov.; and (iii) name and describe five new species.