Early in embryonic development a genetic trigger determines which organs, ovaries or testes, develop from a bipotential primordium. While sex determination is well studied in mammals and birds, no transcriptome-wide studies are available for reptiles. Our recent work shows that interpretation of putative mechanisms in reptiles cannot depend on lessons drawn from mammals. The central player of the mammalian and bird male trajectory, SOX9, does not play a role in our reptile model P. vitticeps until a later stage. While two male genes, AMH and DMRT1, are early acting in P. vitticeps, but play only a later role in mammals. We define for the first time a reptilian genetic sex determination network and show through integration of transcriptome and DNA methylome datasets that the expression of key sex differentiating genes is regulated via differential DNA methylation in male and female gonads.