Red bean, also known as azuki bean [Vigna angularis (Willd.) Ohwi & Ohashi], belongs to a group of legumes (family Fabaceae). The name azuki is a transliteration of the native Japanese name from the Chinese word Shōzu, which means small bean. In Korea, it is known as pat. In total, 178 red bean accessions were taken to analyse the genetic diversity, population structure and gene flow using 39 polymorphic simple sequence repeat markers. A total of 431 alleles were detected, with an average of 11 alleles per locus, among the 178 tested red bean accessions. Forty-six specific alleles were identified with 20 loci. Locus CEDG090 had the highest number (n = 22) of alleles, whereas only two alleles were observed at loci CEDG144 and CEDC018. The proportion of different alleles for microsatellite loci was analysed using a microsatellite toolkit. In locus CEDG029, one allele was shared in all the three groups of varieties and species, and three alleles were shared between the wild ancestors and cultivated varieties, while in locus CEDG090, one allele was shared in all the three groups and 12 alleles were shared between the wild ancestors and cultivated varieties. Our findings describe the genetic relationships and population structure of the red bean in Korea and will be useful for designing effective breeding programmes and broadening the genetic base of commercial varieties. Moreover, the results demonstrate substantial gene flow from the red bean to nearby wild relatives in a given region.