The adaptive significance of polyploidy has been extensively debated and chromosome level genome assemblies of non-model polyploids can provide insight into this topic. The Australian grass, Bothriochloa decipiens, belongs to the BCD clade, a group with a complex history of hybridization and polyploidy. We sequenced, assembled and annotated a chromosomal level genome reference of Bothriochloa decipiens using linked read sequencing and proximity ligation scaffolding. Comparative analysis revealed that the species is a diploidized allotetraploid. We grouped the 20 major scaffolds, representing the 20 chromosomes, into the two subgenomes of the parental species using unique repeat signatures. We found evidence of biased fractionation as well as differences in the activity of TEs between the subgenomes prior to hybridization. Genes retained as duplicates were enriched for biological functions such as transcription and response to external stimuli such as drought, supporting theories of biased duplicate gene retention following WGD events. This is a widespread species with the ability to establish well on many soil types easily, making it useful for ecological restoration of Australian grasslands. This reference genome is a valuable resource for future population genomic research involving Australian grasses which may be helpful in decision making during the ecological restoration processes.