A genome-wide bacterial artificial chromosome (BAC) physical map of the apple, Malus domestica Borkh., has been recently developed. This study addresses development of SSR markers from the BAC-end sequences in apple. Previously designed 187 BAC-SSR primer pairs were subjected firstly to gradient-PCR for amplification and to determine their optimum annealing temperatures. Then, the amplified primer pairs were tested in two F1 segregating populations: ‘Kasel-37’ x ‘Delbarestivale’, and ‘Kasel-41’ X ‘Williams Pride’. The PCR reactions were performed in 12 F1 progenies and in the parents to determine segregation types of the primer pairs. There was no amplification in 20 SSR primer pairs, and 87 of them were monomorphic in the two populations. As a result, 80 of the primer pairs showed segregation in each of the two F1 populations