Each generation of high-throughput sequencing technologies has simplified genome assembles for nontraditional model species. The order that species were selected for genome sequencing roughly depended on the available wealth of historical information, economic importance, conservation status, or general public interest. These initial assemblies rarely approached the quality of species like human or mouse due to the still high absolute cost of sequencing, diminishing returns of deeper coverage when using a single platform, and lack of computational resources. However, each subsequent generation of sequencing technologies and corresponding changes to assembly strategies have generated genome assemblies that approach the quality of human and mouse genome assemblies using a continually decreasing amount of resources. While this reduction in expenses has led to genome assemblies of other species, it also affords an opportunity to improve the genome assemblies from species targeted in the initial wave. One species that would benefit from including data from more modern sequencing technology is the tammar wallaby (Macropus eugenii), in large part due to the wide use of this species in comparative genomics and the large number of associated genomic and biological datasets. Using a combination of sequencing approaches and platforms, we have derived a significantly updated genome assembly for M. eugenii. The new genome assembly represents a significant improvement over the initial published assembly. Our assembly, compared to the initial, has an N50 of 42 MB vs 34 KB; we were able to reconstruct 92% of core eukaryotic genes vs 37% in the earlier assembly. RNAs from 17 different tissues were sequenced and used to annotate 30,342 genes. Further sequencing of male and female M. eugenii genomic samples was used to identify autosomal and X-linked scaffolds. Using these data, we have analyzed the differential conservation and rates of evolution of sex-linked genes in eutherian and marsupial lineages.