Two invasive mussel species are known from South Africa, Mytilus galloprovincialis and Semimytilus algosus. Most of the existing research on these invaders has focused on the intertidal zone, with little attention paid to subtidal habitats. This study addresses this knowledge gap by quantifying the relative abundance and size of native and alien mussels from the high-shore down to the subtidal zone, while accounting for the effects of wave exposure. This was achieved through extensive surveys along the west coast of South Africa and the Cape Peninsula. At all shore zones, mussel abundance varied among species and wave exposures. In intertidal habitats, invasive species were recorded in greatest abundances at wave-exposed sites. Specifically, M. galloprovincialis was dominant in the high-shore, but this pattern changed down the shore. In the mid-shore, the invaders were equally dominant over native mussels, while in the low-shore S. algosus became the most abundant. Notably, the native Choromytilus meridionalis was absent intertidally. In the subtidal zone M. galloprovincialis was rarely present, whereas S. algosus maintained a strong presence. The maximum size of native Aulacomya atra and invasive S. algosus in the subtidal zone was roughly double that recorded in the intertidal zone. Importantly, these results highlight that observations made from intertidal studies of mussel invasions cannot be used to infer subtidal patterns.