The genetic basis of parallel evolution has been revealed in recent studies. However, the spatial scale of parallel origins of the similar phenotype is not well understood. Here we investigated geographic variation in trichome phenotype (hairy and glabrous) of Arabidopsis halleri subsp. gemmifera in a small area in the Kansai region, central Japan. We also explored the association of trichome variation with polymorphism of the candidate trichome gene GL1. The glabrous phenotype tended to dominate in the study area, but the relative frequency of the glabrous phenotype varied considerably among local populations. GL1 was sequenced for 120 glabrous plants from 13 populations, and 16 putative loss-of-function mutations were found. Furthermore, 14 of them occurred within the radius of 50 km, and 9 were within the radius of 25 km. None of 75 hairy plants from 8 populations was homozygous for frameshift or premature stop mutations. Thus, the glabrous phenotype was strongly associated with the putative loss-of-function mutations in GL1. Our results suggest that parallel evolution of the same phenotype can occur in a much smaller spatial scale than previously expected.