Microsatellites were identified from three fully sequenced Y chromosome-specific bacterial artificial chromosome clones from the tammar wallaby, Macropus eugenii. Ten microsatellites were genotyped in male tammar wallabies. Four loci were polymorphic with between two and six alleles per locus. Eleven different haplotypes were identified from 22 male tammar wallabies. No amplifications were obtained from female samples. Each microsatellite was also shown to amplify reliably in at least one other macropod species. These markers may therefore prove useful as some of the first male-specific genetic markers for marsupials, with potential application to studies of male-biased dispersal and mating systems.