| Summary: | The family Gymnophthalmidae is one of the most speciose lineages of lizards in the Neotropical region. Despite recent phylogenetic studies, the species diversity of this family is unknown and thus, its phylogenetic relationships remain unclear and its taxonomy unstable. We analyzed four mitochondrial (12S, 16S, Cytb, ND4) and one nuclear (c-mos) DNA sequences of <i>Pholidobolus anomalus</i>, <i>Cercosaura manicata boliviana</i> and <i>Cercosaura</i> sp., using the maximum likelihood method to give insights into the phylogenetic relationships of these taxa within Cercosaurinae. Our results suggest that <i>Pholidolus anomalus</i> is nested within the clade of <i>Cercosaura</i> spp., that material we collected near Oxapampa belongs to a new species of <i>Cercosaura</i>, and that lizards identified as <i>Cercosaura manicata boliviana</i> belong to a separate lineage, possibly a new genus. We assign <i>Pholidobolus anomalus</i> to <i>Cercosaura</i>, redescribe the species, and designate a neotype to replace the lost holotype. In addition, we describe the new species of <i>Cercosaura,</i> and comment about the taxonomic status of “<i>Cercosaura manicata boliviana”</i><i>incertae sedis</i>.
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