A precipitous increase in the abundance of the corallivorous snail Drupella cornus at Ningaloo Reef, Western Australia, raises fundamental questions about the population structure and genetics of this species. We examined genetic heterogeneity at ten polymorphic allozyme loci among samples of adult D. cornus from nine sites along 180 km of Ningaloo Reef, plus two sites from the Abrolhos Islands and one from the Dampier Archipelago, spanning a total distance of 1170 km. Variations in allelic frequencies were small (average F-ST=0.007), indicating that a high degree of planktonic dispersal is the norm. Nevertheless, some heterogeneity among samples was found at four of the loci. This heterogeneity occurred within Ningaloo Reef and did not increase with geographic distance. The local heterogeneity was not a function of habitat type but seemed to be associated with stage of outbreak. However, all outbreak populations came from within Ningaloo Reef and the non-outbreak populations were from outside Ningaloo Reef proper. Our results show peculiarities in the genetic structure of D. cornus on Ningaloo Reef, but the causes are not understood.