We present the genome sequence of the Central Bearded Dragon, Pogona vitticeps, which is a member of the Agamidae and the first representative of the Australian squamates to be sequenced. The dragon lizard has many unusual biological characteristics, including a ZZ/ZW mode of sex determination, involving a sex micro-chromosome pair, with coincident sex reversal by incubation temperature. As such, it provides a model for the study of sex determination in reptiles, and in particular, the evolution of interactions between environment and genotype in determining offspring sex. This sequence builds our knowledge of squamate genome organisation and evolution, through comparison with the Anolis genome, the two lizards having diverged approximately 146 Mya.