Acer mono Maxim. is one of the major components of cool temperate forests in Japan. Some of its many varieties are distributed sympatrically. Because of its great variability, the intraspecific taxonomy and nomenclature of the species are controversial. To understand the genetic relationships among these varieties and whether hybridization or introgression occurred among the sympatric varieties, we studied the genetic relationships among sympatric varieties of A. mono in the Chichibu Mountains(A. mono var. ambiguum, A. mono var. connivens, A. mono var. marmoratum) and Central Hokkaido(A. mono var.mayrii and A. mono var. glabrum) in Japan. Our results showed that varieties in Chichibu are genetically close,suggesting that hybridization or introgression might occur between these varieties, which could explain the higher genetic diversity of varieties in Chichibu than in Hokkaido.In contrast to the close relationships between the varieties in Chichibu, varieties in Hokkaido seemed relatively separated from each other; indeed, there may be reproductive isolation between the two varieties. The results provide new insight for the taxonomy of the varieties of A. mono,especially the sympatric varieties, in Japan. One of the major components of cool temperate forests in Japan. Some of its many varieties are distributed sympatrically. Because of its great variability, the intraspecific taxonomy and nomenclature of the species are controversial. To understand the genetic relationships among these varieties and whether hybridization or introgression occurred among the sympatric varieties, we studied the genetic relationships among sympatric varieties of A. mono in the Chichibu Mountains (A. mono var. ambiguum, A. mono var. connivens, A. mono var. marmoratum) and Central Hokkaido (A. mono var. maryi and A. mono var. glabrum) in Japan. Our results showed that varieties in Chichibu are genetically close, suggesting that hybridization or introgression might occur between varieties, which could explain the higher genetic diversity of varieties in Chichibu than in Hokkaido. In contrast to the close relationships between the varieties in Chichibu, varieties in Hokkaido seemed relativ indeed, there may be reproductive isolation between the two varieties. The results provide new insight for the taxonomy of the varieties of A. mono, especially the sympatric varieties, in Japan.