We report the development of 48 anonymous nuclear loci from the Australian skink Tiliqua rugosa using 454 sequencing. These loci amplified across a Western Australian lineage (47 loci), a ‘northern’ lineage (48 loci) and a ‘southern’ lineage (46 loci). We further tested amplification for the related T. adelaidensis and Egernia stokesii where 37 and 34 loci amplified respectively. The loci showed variability within T. rugosa (22 polymorphic loci) and at least 27 loci also exhibited variation among the three species, highlighting the usefulness of these markers for phylogenetic, phylogeographic and population genetic analyses in T. rugosa and related species.