PCR-based molecular markers were used to map the recessive branching gene (b1) and the fertility restoration gene (Rf1) in sunflower. Sixty-one dominant RAPD markers, generated by 31 random primers, as well as 14 STS markers, were analyzed among an F2 population (C3) of 230 plants derived from cross RPG01 x AEHC1. Fourteen STS markers were analyzed in a second population (C4) of 211 plants from the cross RPG01 x R300V. Ten STS markers were analyzed in both populations. A linkage map of 64.6 cM containing the bl locus, 9 RAPD markers and 2 codominant STS markers was identified using JOINMAP based on segregation data. An RAPD marker, UBC105_740. was mapped at 5 cM from the gene bl. Another linkage group of 34 cM, containing the male fertility restoration locus Rfl as well as one RAPD and one STS marker, was also identified. The STS markers could be easily integrated into the previously established sunflower RFLP maps and should permit to verify the identity of branching and fertility restoration genes of different origins.