The population structure of the redclaw crayfish (Cherax quadricarinatus) was investigated by analyses of allozymes and RAPD (randomly amplified polymorphic DNA) markers. Electrophoretic analysis of 28 enzyme loci in 12 redclaw populations from the Northern Territory (NT) and North Queensland (NQ) revealed generally low estimates of heterozygosity within each population and low estimates of genetic differentiation among populations except for a fixed allelic difference at the carbonic anhydrase (CA*) locus between NT and NQ populations. Low levels of genetic variability among the NQ populations is possibly a reflection of their recent radiation across the Gulf of Carpentaria after its inundation between 18000 and 6000 BP. RAPD analysis of seven redclaw populations could distinguish each river population and also grouped them according to geographic proximity. RAPD analyses also revealed significant genetic variability both within the species and within individual populations, which could be used to improve their culture. On a preliminary scale, RAPD fragments provided a useful tool for differentiating redclaw strains and constitute a marking system that could be used in crayfish genetic improvement programmes.