Sunflower rust (Puccinia helianthi) emerged as a serious disease in North America in the last few years. RHA 464, a newly released sunflower inbred line, was identified to resist the most predominant and virulent rust races. The objectives of this study are to determine the chromosome location of this resistance and molecularly mark the resistance gene. RHA 464 was crossed with HA 89 (a highly rust susceptible inbred line) and F2 seedlings were tested for segregation of rust resistance. Rust resistant genotypes of F2 individuals were confirmed with segregation of F2:3 families. The results indicated a single dominant gene confers the rust resistance in RHA 464, and this gene was designated as R12. We used 870 previously mapped SSR markers of sunflower to make bulked segregant analysis. Subsequent F2 genotyping mapped R12 on linkage group 11. SSR marker CRT275 was the closest marker linked to R12 with genetic distances of 1.0 cM. R12 is unlinked to other known rust resistance genes in sunflower, indicating a novel rust resistance locus.