In the present study, we investigate the potential impact of the first proposed interstate translocation of mussel spat, for aquaculture enhancement, on the genetic integrity of Mytilus populations in Western Australia (WA). We performed genetic analysis on four populations (Garden Island, Bunbury, Albany and Esperance) in WA and on mussels from three hatcheries in South Australia (SA), Victoria (Vic) and Tasmania (Tas) proposed as spat sources in the translocation application. Two genetically distinct groups of M. galloprovincialis were identified, which corresponded to introduced Northern Hemisphere and native Southern Hemisphere haplotypes. Mussels obtained from the hatcheries showed a marked proportion of native haplotypes, while mussels of three (Garden Island, Bunbury and Esperance) of the four sampled WA Mytilus populations consisted mostly of introduced haplotypes. Most importantly, all samples were notable for a mixture of native and introduced haplotypes with the great majority of introduced haplotypes occurring in both WA and eastern states samples. Based on these results, it seems unlikely that the proposed translocation of mussel spat could negatively impact WA Mytilus populations. The current study presents valuable information regarding the genetic composition of Mytilus populations and will prove useful in the assessment of future translocation applications and biodiversity of mussel species in WA. © CSIRO 2014.