A multidisciplinary approach has been applied to examine the population structure of sardine Sardinops sagax off South Africa, where this species supports significant fisheries and is also of ecological and eco-tourism importance. Observations of discontinuous sardine distribution patterns, discrete spawning grounds and significant spatial differences in a variety of phenotypic characteristics have suggested the existence of discrete western, southern and eastern sardine sub-populations or stocks. The use of parasites as biological tags to elucidate sardine population structure has recently been investigated, and strong spatial gradients around South Africa in the prevalence, mean infection intensity and mean abundance of a digenean ‘tetracotyle’ type metacercarial endoparasite considered to be of the genus Cardiocephaloides and found in the humours of fish eyes support and have proved particularly convincing evidence for the sardine multiple stock hypothesis. A discontinuous distribution in the occurrence of another parasite, the coccidean Eimeria sardinae found in fish testes, has provided additional but weaker evidence of discrete stocks. These results have contributed to a changed understanding of the population structure of South African sardine and have significant implications for management of the fisheries for this species.