Two morphologically distinctive, monotypic genera of Australian agamid lizards, Moloch and Chelosania, are of uncertain relationship to the main Australian arid zone radiation, the amphiboluroids. We report that the karyotypes of both Moloch horridus and Chelosania brunnea are both 2n  =  36 with six pairs of macrochromosomes and 12 pairs of microchromosomes. This is probably the plesiomorphic karyotype for agamids, and different to the 2n  =  32 karyotype (10 pairs of microchromosomes) that is a synapomorphy of the amphiboluroids. This finding supports recent DNA sequencing studies of Australian agamids that find an early origin and independent branching position for these two genera. Both genera therefore seem to have no special relationship with the amphiboluroids, indicating colonization of the arid habitats by more than one lineage of agamids at an early stage of their diversification on the Australian continent.