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The use of bivalves such as the brown mussel (Perna perna) and the black mussel (Choromytilus meridionalis) is common in the study of marine pollution and the effect of these pollutants on ecosystems and are important in both economic and ecological roles. Namibian marine ecosystems are threatened by pollution from mining, commercial fishing and population growth. The aims of this study were to determine baseline metal concentrations, spatial variation and variation between species. Metal levels in C. meridionalis from Guano Platform (GP) are the lowest of all the sites. The most polluted sites are Rocky Point (RP), Halifax Island (HIL) and between Walvis Bay and Swakopmund (WS). The bioaccumulation of metals between P. perna and C. meridionalis were not uniform for all metals. Overall the study indicates the condition of the coastline to be mostly normal, with Cd and Pb levels being of concern.