The exclusively coastal Cakile maritima and Eryngium maritimum represent a linear biogeographical system. Genetic variation among 25 individuals of C. maritima and 16 individuals of E. maritimum, from the coasts of Europe, North Africa and the Canary Islands, was analysed using random amplified polymorphic DNAs (RAPDs) and intersimple sequence repeats (ISSRs). Genetic distances (Dice) were calculated and used to investigate the correlation between genetic and geographical distances, to construct Neighbour Joining (NJ) trees, and to compare mean genetic distances between areas within and across species. Genetic distances and geographical distances measured along the coast are well correlated in Cakile and Eryngium. This implies that dispersal in both species is largely along the coast. The NJ analyses resulted in the recognition of Atlantic and Mediterranean clusters in both Cakile and Eryngium. The genetic distance between these two clusters is much larger in Eryngium (0.285) than in Cakile (0.037). Mean genetic distances are substantially higher in the Mediterranean than in the Atlantic clusters in both species, and higher in Cakile than in Eryngium particularly in the Atlantic cluster. It is argued that all similarities and differences between the two species can be explained with the presumed distribution of the two species in the Würm glacial as reconstructed from their extant temperature requirements, the distribution of ice cover, permafrost, and sea surface temperatures in that period, and indirect fossil evidence.