We investigated the geographical distribution of genetic variation in 67 individuals of Triglochin maritima from 38 localities across Europe using AFLP markers. Analysis of genetic variation resulted in the recognition of two major genetic groups. Apart from few geographical outliers, these are distributed (1) along the Atlantic coasts of Portugal, Spain and France and (2) in the North Sea area, the Baltic Sea area, at central European inland localities, the northern Adriatic Sea coast and the Mediterranean coast of southwest France. Considering possible range shifts of T. maritima in reaction to Quaternary climatic changes as deduced from the present-day northern temperature limit of the species, Quaternary changes of coastline in the North Sea area and the very recent origin of the Baltic Sea, we conclude that the coastal populations of T. maritima in the North Sea and Baltic Sea areas originated from inland populations.