We used the geographic distribution of genetic diversity in the beach pea, Lathyrus japonicus (Leguminosae) to reconstruct the location of a Pleistocene refugium and Holocene range expansion. DNA sequence data for the chloroplast ndhF-trnH spacer from a global sample of 22 populations in Asia, North America, and Europe were used to assess broad-scale, circumpolar patterns. The cpDNA data revealed five haplotypes including two largely allopatric, widespread haplotypes (one Pacific, the other Atlantic and inland in the Great Lakes). Three geographically restricted haplotypes were also recovered: one each in New Jersey, Lake Champlain, and the Pacific Northwest. The distribution of isozyme variation at 14 loci for 38 populations of beach peas from the Atlantic and Pacific coasts of North America, Lake Champlain, and the Great Lakes was used to reconstruct a North American history. One subset of allozymes was found on the Atlantic Coast and in the Great Lakes; a second subset was widespread from northwestern North America to Newfoundland. There was a nested pattern to the localization of allozymes along the Atlantic Coast; Cape Cod had the greatest number of allozymes. Pacific and Atlantic isozymes and cpDNA haplotypes occurred together along the coast of Newfoundland and adjacent Labrador. The pattern of genetic variation as assessed from isozymes and cpDNA allow the inferences that: 1) an early divergence yielded Atlantic and Pacific lineages and 2) the Atlantic lineage occupied a Wisconsinan refugium on the now-submerged coast of northeastern North America. Our evidence is consistent with there being Holocene secondary contact between the Atlantic and Pacific lineages in the area where they now overlap. We also suggest that an early post-glacial vicariance event is implicated in the history of the Lake Champlain populations.