Abstract
Common carp Cyprinus carpio were introduced into Australia on several occasions and are now the dominant fish in the Murray‐Darling Basin (MDB), the continent's largest river system. In this study, variability at 14 microsatellite loci was examined in C. carpio ( n = 1037) from 34 sites throughout the major rivers in the MDB, from 3 cultured populations, from Prospect Reservoir in the Sydney Basin and from Lake Sorrell in Tasmania. Consistent with previous studies, assignment testing indicated that the Boolara, Yanco and koi strains of C. carpio are present in the MDB. Unique to this study, however, the Prospect strain was widely distributed throughout the MDB. Significant genetic structuring of populations (Fisher's exact test, AMOVA and distribution of the different strains) amongst the MDB sub‐drainages was detected, and was strongly associated with contemporary barriers to dispersal and population history. The distributions of the strains were used to infer the history of introduction and spread of C. carpio in the MDB. Fifteen management units are proposed for control programmes that have high levels of genetic diversity, contain multiple interbreeding strains and show no evidence of founder effects or recent population bottlenecks.