The Japanese oyster Crassostrea gigas forms the mainstay of the South African oyster farming industry. Despite having been cultured along the South African coast for 30 years, this is the first record of naturalized populations of this well known global invader from the region. DNA sequence data confirmed the presence of C. gigas in the Breede and Goukou estuaries. Populations of 184,206 ± 21 058.9 (SE), 876 ± 604.2 (SE) and 1 228 ± 841.8 (S.E.) individuals were recorded in the Breede, Goukou and Knysna estuaries respectively. No C. gigas were recorded from the open coast. The condition index of oysters in the Goukou and Knysna estuaries differed significantly from those in the Breede Estuary (Kruskal-Wallis ANOVA H = 48.249, P < 0.01) but no difference was found between the Goukou and Knysna estuaries (Kruskal-Wallis ANOVA H = 48.249, P > 0.05). The lower condition index recorded in the Breede Estuary is believed to reflect decreased food supply as a result of the large C. gigas population present in the estuary.