Three taxa of the malaria mosquito Anopheles balabacensis complex representing three geographical regions (Thailand, Peninsular Malaysia and Sabah) in Southeast Asia, were analysed for genetic variation at 15 gene-enzyme systems. The Sabah taxon was monomorphic for all the 15 gene-enzyme systems. Only two gene-enzyme systems (esterase and glucose phosphate isomerase) were variable in the Thailand and Peninsular Malaysia taxa. The average heterozygosity or gene diversity was 0.007 for the Thailand taxon and 0.028 for the Peninsular Malaysia (Perlis) taxon. There were no unique gene-enzyme markers in the three taxa studied. The average values of genetic identities (0.933-0.997) and genetic distances (0.003-0.069) indicate that these three taxa are of subspecific status.