Exposed intertidal sandy beaches are commonly dominated by surf clams of the genus Donax. In Peru and Chile these bivalves play an important role for artisanal fisheries. Beside that, little is known about the taxonomy, biology, and the clams susceptibility to climatically induced changes. The taxonomic status of the two Donax species Donax marincovichi and Donax obesulus, distributed along the Peruvian coastline, is controversially discussed. As morphometric comparisons reveal no significant differences we possibly deal with a single rather than with two species. Furthermore, our knowledge on larval dispersal allowing gene flow among populations is scarce. Therefore, both putative Donax species were sampled at ten beaches along the coastline from northern Chile to northern Peru. Partial cytochrome oxidase I sequences were analysed in order to estimate the genetic distances between both putative species and to estimate the intraspecific gene flow along the coastline. Region specific patterns and the dependence on recruitment of local stocks are discussed.