Capelatus prykei gen. et sp.n., a distinctive new lineage of copelatine diving beetle, is described from the greater Cape Town area of the Western Cape Province, South Africa, on the basis of both morphological and molecular data. The genus-level phylogeny of Copelatinae is reconstructed using a combination of nuclear and mitochondrial DNA regions, demonstrating that Capelatus gen.n. has no close relatives within the Afrotropical region, instead forming a clade with the Palaearctic Liopterus and largely Australasian Exocelina. Capelatus gen.n. apparently represents a striking example of a phylogenetically isolated Cape lineage, which also appears to be narrowly endemic and endangered by ongoing habitat loss.