The tammar wallaby (Macropus eugenii) has a 2n = 16 karyotype with an XX/XY female/male sex dimorphism. Female reproduction can be manipulated to produce up to five offspring per year. We have crossed two genetically distant subspecies of tammars, one from Kangaroo Island in South Australia, the other from Garden Island in Western Australia, to produce fertile F1 offspring of both sexes. Male F1 hybrids were crossed with female Kangaroo Island tammars to produce over 80 phase-known backcross progeny for linkage studies. Here we report detection of two linkage groups derived from these male recombination values. The first consists of alpha-lactalbumin and an anonymous tammar cDNA clone, pB72; the second contains the gene for a marsupial-specific milk protein (late lactation protein), the gene for lipoprotein lipase, and an anonymous cDNA clone, pB65. The gene for late lactation protein has previously been assigned to tammar chromosome 3.