Derived from Korean male sterility, msK is valuable for pepper breeding using the Genic Male Sterility (GMS) because very stable for sterility. We performed development of molecular marker in a segregating population of the msK. We performed RAPD using bulked segregant analysis. One RAPD primer was identified as tightly linked to the locus at about 1.2cM. On the basis of sequence which amplified by BSA-RAPD, a primer set was designed and amplified specific bands on MF and MS. We converted to the cleavage amplified polymorphic sequence (CAPS) marker from the specific band. This CAPS marker will be useful to produced F1 hybrid seeds using the msK.