Poxviruses are large DNA viruses with varying zoonotic potential that have been recognised in a broad range of wildlife taxa including birds, reptiles, marine mammals, marsupials and primates. Although pox lesions and poxvirus-like particles have been detected in red kangaroos as well as eastern and western grey kangaroo species, their genetic relationships to poxviruses in other animals and humans is not understood. Here, we present the first genome sequence of a marsupial poxvirus, the Grey kangaroo poxvirus (GKPV), isolated from a wild eastern grey kangaroo. In the present study, histopathologically confirmed epidermal pox lesions were used to recover the complete viral genome sequence by next generation sequencing technology. Subsequent analysis of the GKPV genome demonstrated the highest degree of sequence similarity with Molluscum contagiosum virus 1 (MOCV1) (44.05%) followed by Squirrelpox virus (41.76%) and Nile crocodilepox virus (40.01%). The novel GKPV complete genome encompasses most of the chordopoxviruses protein coding genes (88) that are required for the genome replication and expression, with only three essential protein coding genes being absent. Instead, the GKPV carries 67 additional genes encoding unknown proteins, many of which are likely to have transmembrane helix and other homologous functions. Phylogenetic and recombination analyses showed that the GKPV is the deepest available candidate genome of chordopoxviruses, and is not closely related to any other Chordopoxvirinae genome so far isolated from other natural host species. This is the first GKPV complete genome sequence from an infected marsupial.