Cytoplasmic male sterility (CMS), is the most valuable system in commercial hybrid seed production in hot pepper. Whereas in sweet pepper (Capsicum annuum var grossum), the unavailability of a stable restorer’s line is one of the major constraints in commercial hybrid breeding. Identifying the markers linked to CMS and nuclear restorer-of-fertility (Rf) genes will help in the production of CMS hybrids in sweet pepper. In the present study, we identified seven markers co-segregating with Rf genes using bulk segregating analysis (BSA) on the F2 Rf-segregating mapping population. Among these, the CRF-SCAR marker proved to be linked to the fertility restorer gene and it could be used for screening of genotypes to identify restorers and non-restorer lines in future Capsicum breeding programs and help in the establishment of CMS system for commercial hybrid seed production.