Tropidurus itambere is an endemic lizard of the Cerrado biodiversity hotspot. We used phylogenomics to investigate cryptic diversity and phylogenetic relationships. T. itambere is paraphyletic and its main clade composed of 5 cryptic species. Species were consistently recovered across all delimitation and phylogenomic methods. Cryptic lineages are usual in Cerrado and its biodiversity grossly underestimated.