Specimens of Imparfinis were recently collected in north-western Argentina from the Bermejo River basin (Salta and Jujuy Provinces), del Valle River (Salta Province) and Horcones River (Santiago del Estero Province). An integrative approach to taxonomy, combining a detailed morphological study and molecular phylogenetic analyses, was applied to determine the species identity of these specimens. A principal components analysis of morphological data clustered the specimens from north-western Argentina and from the Amazon basin, indicating a close morphological resemblance. Also, a molecular phylogenetic analysis showed populations of I. guttatus from Argentina and Peru forming a clade. According to the conducted haplotype network analysis these populations are distinct in two mutations. Thus, in the absence of morphological or molecular data indicating the contrary, the combined method supports the identity of the specimens from the tributaries of the Paraguay River in Argentina as I. guttatus, whose type locality is in the upper Beni River basin in Bolivia. This contribution is also the first record for this species from Argentina. The disjunct distribution of I. guttatus provides new evidence reinforcing the hypothesis for the origin of the Paraguayan ichthyofauna. We also provide an approach to the phylogenetic relationships of Imparfinis in Heptapteridae.