An analysis of cytoplasmic crossing type variation in Australian populations of Culex quinquefasciatus, a member of the Culex pipiens complex of mosquitoes, revealed high levels of variability causing partial incompatibility between natural populations. Segregating crossing types were commonly found together within sampled sites. No correlation was evident between similarity of crossing type and environmental parameters of the sites, nor distance between sites. The nature of the observed variation did not support the hypothesis of paternally expressed nuclear 'restorer' genes. Such high levels of crossing type variation would be likely to impede attempts to control populations of the Culex pipiens complex using cytoplasmic incompatibility.