Native American Artemia franciscana has become an introduced species in the Old World due to the rapid development of the aquaculture industry in Eurasia. The recent colonisation of A. franciscana in Mediterranean regions and Asia has been well documented, but Australia is a continent where the dispersal of this species is not well understood. In the present study, we sequenced the cytochrome oxidase subunit I (COI) and examined the phylogenetic relationships, haplotype network and population genetic structure of Artemia from four geographical localities in Australia and two American native localities. Our results confirmed the colonisation of Australia in all four localities by A. franciscana. First, we document the occurrence of Artemia in Mulgundawa and St Kilda localities in Australia. The Dampier population is a monomorphic population, but there is high genetic variation and a degree of demographic expansion observed in other introduced A. franciscana populations in Australia. This observation suggests an interaction between environmental conditions and adaptive potentials of A. franciscana. Our findings imply that populations from St Kilda and Port Hedland might have originated from a San Francisco Bay source, while the two other locations resulted from admixture between Great Salt Lake and San Francisco Bay sources, perhaps resulting from secondary introduction events.