Sequencing of the tammar wallaby (Macropus eugenii) genome has the potential to be an extremely valuable resource for investigating evolutionary and developmental aspects of the mammalian immune system. However, the tammar wallaby genome has only been sequenced to a 2-fold depth and consists of small contigs, leaving many sequence gaps, many putative orthologs unpredicted and the location of genes within the genome unknown. In the case of low sequenced genomes, physical maps of genes on chromosomes can help identify specific genes if they map to conserved regions. Genes corresponding to adaptive immunity have been mapped in the tammar wallaby; however, genes corresponding to the innate immune system have not been investigated. We predict 2 types of genes important to the innate immune system, mucins and lysozymes, in the tammar wallaby and compare the predicted peptide sequences and locations of the genes with the South American opossum (Monodelphis domestica) and human. We use fluorescence in situ hybridization to physically map the genes to tammar wallaby chromosomes, demonstrating the importance of identifying and mapping genes when genomes have low sequence coverage. As mucins and lysozymes play protective roles in young animals, we also propose that their immunological role in developing marsupials warrants further investigation.