Polyploidisation is a major driver of plant evolution. Arabidopsis, the genus of the model plant A. thaliana, has been diversified by both auto- and allo-polyploidisation. Northern rock-cress A. lyrata petraea is known to have two cytotypes, diploid and tetraploid, although minority cytotype disadvantage is often assumed for a species which generated a new cytotype. We studied geographic distribution pattern and genetic structure of those cytotypes in its northwestern distribution range to understanding the origin of tetraploid and how two cytotypes are maintained. We used 32 microsatellite loci to identify cytotypes and this was verified by flow cytometry. Tetraploid plants were widespread in British Isles whereas it was negligible in Iceland, Norway and Sweden. The diploids and tetraploids were genetically distinct from one another and gene flow between them appeared to be highly limited despite common sympatric existence. Tetraploids showed high inbreeding coefficient and high intra-population relatedness but also reasonably high genetic diversity comparable to diploid populations from the same areas. These results suggest the single origin of tetraploids and strong reproductive barrier between cytotypes in the study area.in the study area.