Map-based cloning of the restorer gene Rf1, responsible for fertility restoration of the PET1 cytoplasm in sunflower, requires tightly linked markers to the gene of interest. Screening 1200 decamer primers by bulked segregant analyses identified seven RAPD markers mapping on the same linkage group as the restorer gene Rf1. In the F2 population of the cross RHA325(cms) × HA342 (183 individuals) one of the RAPD markers, OPK13_454, mapped 0.9 cM from Rf1, followed by OPY10_740 with 2.2 cM. Bulked segregant analyses using 1024 AFLP primer combinations identified 282 polymorphisms in 203 primer combinations. Selected single plants from the bulks and recombinant plants were screened to further reduce the number of primer combinations to be mapped in the F2 population. The map for the linkage group carrying the restorer gene now consists of 43 markers (7 RAPD-, 1 SSR-, and 35 AFLP-markers) and covers 191.9 cM. E32M36_155 and E44M70_275 were mapped 0.7 cM and 0.1 cM from the restorer gene, respectively. Two of the RAPD markers, OPK13_454 and OPY10_740, were successfully converted into SCAR markers, HRG01 and HRG02, respectively. Amplification of the markers OPK13_454/ HRG01 and OPY10_740/HRG02 was investigated for a set of 11 restorer and nine maintainer lines of PET1. For cloning the restorer gene Rf1, colony hybridizations against high-density BAC filters of our sunflower BAC library and 3D-PCR pooling strategies were used to identify positive BAC clones. BAC fingerprinting using different restriction enzymes in combination with hybridizations was performed to develop a contig around the restorer locus Rf1.