The wheat curl mite (WCM), Aceria tosichella Keifer, is an eriophyoid pest of cereals, and the vector responsible for transmitting wheat streak mosaic virus. Several authors have suggested cryptic species of this mite identified through morphological variation, but this has never been conclusively demonstrated. Here, we use the mitochondrial 16S rRNA gene and two nuclear markers (internal transcribed spacer 1 and adenine nucleotide translocase) to show that WCM from Australia consists of at least two separate lineages that may represent putative species. In our study, both WCM variants were widespread and the only eriophyoids found on wheat varieties. The WCM variants were also found on alternate host plants, including some plants not known to host WCM. These results have implications for the control of this pest within Australian cereal crops.