The karyotypes of Malagasy geckos are poorly known. Herein, we describe the karyotypes of two Malagasy gecko species, Paroedura picta and an undescribed or currently unrecognised Paroedura species. These are the first karyotypes described for the genus Paroedura. Each species had a distinct karyotype; P. picta had 2n=36 and Paroedura sp. had 2n=34. We used a fragment of the mitochondrial ND2 gene to conduct a phylogenetic analysis of 17 described and putative Paroedura species and show that the Paroedura sp. examined here is unique and related to P. bastardi, P. ibityensis, P. tanjaka and another undescribed Paroedura species from Tsingy de Bemaraha. Our results highlight the need for continued research into the basic biology and taxonomy of Malagasy lizards.