The surf clam Donax serra (Bivalvia, Donacidae) dominates sandy beach communities of two southern African biogeographical regions, a cold (Benguela current) and warm province (Agulhas current). Morphometric and behavioural differences led to a controversial discussion of whether or not populations from the two provinces belong to the same species. Shell size measurements confirmed morphological differences: clams from the cold province were significantly rounder, flatter and less wedge-shaped than clams from the warm province. In this study a genetic approach was used to relate phenotypic differences to genetic variability of four populations of D. serra separated by up to 2 500 km of shoreline. Genetic analysis of twenty-two protein-coding loci was carried out by starch-gel electrophoresis. Populations studied are conspecific (genetic distances range from 0.003 to 0.044) and possess genetic variation (alleles per locus: 1.73 - 1.91; mean heterozygosity: 18 - 22%; percentage polymorphism: 45.5 - 59.1%) in the range of most other marine bivalves, which allows for potential adaptation to environmental changes. Wrights fixation indices show little to moderate genetic divergence among the subpopulations relative to the limiting amount under complete fixation (FST = 0.016 - 0.089), moderate divergence of individuals relative to the total population (FIS = 0.265 - 0.452), and comparably high divergence of individuals relative to the compound population (FIT = 0.300 - 0.473). The effective number of individuals exchanged between populations in each generation is high enough (1.44 - 8.65) to counteract genetic drift. We propose that the observed differences represent phenotypic plasticity enabling this species to inhabit different biogeographic regions. Gene flow, balanced selective pressure and evolutionary inertia are discussed as explanations for similarities of the two outlying populations. The substantial subdivision of the two Namibian populations indicates a potential biotic barrier and requires separate studies of the population dynamics.