Intra‐ and interspecific genetic diversity of the lizard species Plica plica (9 localities) and Plica umbra (19 localities) from the Brazilian Amazon was analysed using two mitochondrial (16S rDNA and CO1) and one nuclear (prolactin receptor – PRLR) genes. We generated a maximum‐likelihood and Bayesian hypotheses of phylogenetic relationships, and using the bPTP and ABGD lineage delimiting methods inferred the most likely number of lineages within each species. Both methods delimited five distinct lineages in Plica plica and six lineages within Plica umbra. The nominal subspecies of Plica umbra was comprised of one lineage, while Plica umbra ochrocollaris was comprised of five lineages. In majority of the cases, lineages were restricted to the interfluves of major Amazonian rivers, and different lineages occupied distinct areas of endemism. Phylogenetic relationships of the lineages are largely concordant with the hypothesized formation of the areas of endemism. The geographic structuring of the clades and the delimitation of these clades as distinct lineages suggest the possibility that these lineages represent species. If the observed diversity of lineages within the genus Plica is characteristic of squamate reptiles of the Amazon region, the diversity of squamates is grossly underestimated.