Salsola tragus sensu lato (Chenopodiaceae) is found throughout Western Australia and is considered to be a weed in both natural and agricultural ecosystems, although the current taxonomic status of this species is not clear. The taxonomic literature reports morphological variation within Australian populations of the weed, indicating that there may be genetically distinct ecotypes or unidentified subspecies present within the species. A genetic and cytological approach was used to detect variation between 22 populations of S. tragus sensu lato in the south-west of Western Australia. Out-groups used in this study included a population of S. tragus L. from the USA and Maireana brevifolia (R.Br.) Paul G.Wilson (Chenopodiaceae) from Lake Grace. Four genetically distinct groups were identified, which were not closely related to the S. tragus out-group (~60% similarity). Further, these groups and a S. australis R.Br. sample from the USA were all diploid (2n = 18), unlike the tetraploid (2n = 36) S. tragus. The predominant wheatbelt weed, group A, which was previously classified as S. tragus ssp. tragus L., was identified as S. australis. This species is probably native to Australia, given its arrival predated European invasion. Further research is required to clarify the taxonomic status of the other three possible taxa and determine their status in relation to S. australis.