A detailed study of electrophoretic, morphological and habitat variation amongst species of Cherax in south-western Australia supported the recognition of only five of the eight species currently recognised and revealed that morphological and habitat variation within these crayfish is more extensive and complicated than was previously realised. Within several species morphological and habitat variation was found to be as great as that between species. Furthermore, a major component of the morphological variability, both within and between species, was found to be associated with habitat variation.Three of the five species of Cherax recognised in this study correspond to the consistently recognised and widespread species, C. preissii Erichson, C. quinquecarinatus (Gray) and C. tenuimanus Smith. The two other species are C. crassimantus Riek and C. glaber Riek which have restricted distributions in the extreme south-west of Western Australia. The species C. glabrimanus Riek and C. neocarinatus Riek could not be distinguished from C. quinquecarinatus, nor could C. plebejus (Hess) be distinguished from C. preissii.On a general level, the results of this study question the value of morphological information in systematic studies of freshwater crayfish. Morphologically based taxonomic studies of freshwater crayfish need to be interpreted with caution because, firstly, taxonomic characters may be far more variable than realised; secondly, morphological and habitat differences cannot necessarily be equated with specific distinctions; and thirdly, genetically distinct species that occupy similar habitats need not be morphologically distinct.