The genus Macropus contains many of the most recognizable kangaroo species, which include the largest living marsupials. Despite being a well-studied group, the phylogenetic relationships within this genus remain poorly resolved. With the development of next generation sequencing, it has become possible to investigate phylogenetic relationships using genome level characters. I will discuss the use of retrotransposons as phylogenetic markers, with a focus on kangaroo evolution. A particular class of retrotransposon – an endogenous retrovirus - has been prolific during the evolution of kangaroos. We have utilized presence/absence information of retrotransposons to shed light on the phylogenetic relationships among members of the genus Macropus, and close relatives, and address the statistical support for retroposon analyses when only a single reference genome is available.