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The Asian green mussel Perna viridis is an invasive Indo-Pacific species recently reported from South African harbours. To verify the invasion, a phylogenetic (and morphological) analysis of green-shelled mussels (n = 39), found in six South African harbours, was conducted using the mitochondrial cytochrome c oxidase subunit I gene (COI). Estimates of genetic distances using the neighbour-joining analysis identified P. viridis only from Durban Harbour. All other green mussels were more than 3.2% divergent from P. viridis and were identified as green-shelled variants of indigenous P. perna. The only reliable morphological differences distinguishing the two species were the poorly developed mantle papillae and the wavy pallial line in P. viridis. The confirmed occurrence of P. viridis in a South African harbour suggests that there is a possible threat of the species becoming established and then spreading onto the open coast and competing with indigenous P. perna.
Keywords: DNA barcoding, mtDNA COI, mussel colouration, Perna perna