Common bean (Phaseolus vulgaris L.) is an important export crop in Kyrgyzstan. Bean common mosaic virus (BCMV) is a seed-born disease that affects this crop and reduces its yield significantly in the country. The aim of this study was to identify virus strain(s) occurring in Kyrgyzstan and breed host plant resistance to BCMV using DNA markers. Susceptible Kyrgyz cultivars (Ryabaya, Kytayanka and Lopatka) were included in a backcrossing breeding scheme for introducing host plant resistance from resistant cultivars (Vaillant and Flagrano). The virus strains were evaluated according to the symptoms of differential cultivars. The virus strain NL6 was found in northern Kyrgyzstan, where farmers grow most of the common bean produced in this country. Two SCAR markers (SW13 and SBD5) were used successfully in marker-aided backcrossing for pyramiding the I and bc-1 2 genes, which provide host plant resistance to BCMV. Resistant BC4F2 offspring carrying the I gene showed hypersensitivity reactions to necrosis inducing NL3 strain after detached leaf-assays. © 2013 Springer Science+Business Media Dordrecht.