We believe this study is the first to consider the genetic and phenotypic divergence between isolates of Haemonchus contortus in Australia. Microsatellite markers have been used to investigate genetic divergence, whilst phenotypic divergence has been considered through individual worm morphology, isolate life history traits and the effect of isolates upon the host. The results are discussed in the context of the likely introduction of H. contortus to Australia, its recent isolation, and the characteristics of sheep and goat farming which might act to either isolate or distribute parasites. We conclude that there is significant observable genetic divergence between isolates of H. contortus in Australia. The divergence may have been under-estimated in this study due to a variety of factors. Phenotypic divergence is also observed, and potentially has significant implications for both economic losses due to haemonchosis on individual properties and for decisions regarding the regulation of stock movements in Australia.