Microsatellites were identified from fully sequenced bacterial artificial chromosome clones from the X chromosome and chromosome 2 of the tammar wallaby, Macropus eugenii. A total of 20 microsatellites were genotyped. Seven X chromosome loci and eight loci from chromosome 2 were polymorphic, with between two and 11 alleles per locus. These markers will facilitate genetic mapping in the tammar wallaby and will have wider applications in macropod population genetics. In particular, X chromosome microsatellites will provide a novel evolutionary perspective from which to view macropod mating systems and gene flow.