Male sterility is an important trait of melon in F1 hybrid seed production. Molecular markers linked to a male-sterile gene would be useful in transferring male sterility into fertile melon cultivars and breeding lines. However, markers linked to the ms-3 gene for male sterility present in melon have not been reported. Our objectives were to identify randomly amplified polymorphic DNA (RAPD) markers linked to the ms-3 gene controlling male sterility using bulked segregant analysis in an F2 population from the melon cross of line ms-3 (male-sterile) × `TAM Dulce' (male-fertile), convert the most tightly linked RAPD marker to the ms-3 gene into a sequence characterized amplified region (SCAR) marker based on a specific forward and reverse 20-mer primer pair, and confirm the linkage of the RAPD and SCAR markers with the ms-3 gene in an F2 population from the cross of line ms-3 × `Mission' (male-fertile). A single recessive gene controlling male sterility was found in F2 individuals and confirmed in F3 families. Two RAPD markers that displayed an amplified DNA fragment in the male-sterile bulk were detected to be linked to the ms-3 gene in the F2 population from the cross of line ms-3 × `TAM Dulce'. RAPD marker OAM08.650 was closely linked to the ms-3 gene at 2.1 cM. SCAR marker SOAM08.644 was developed on the basis of the specific primer pair designed from the sequence of the RAPD marker OAM08.650. The linked RAPD and SCAR markers were confirmed in the F2 population from the cross of line ms-3 × `Mission' to be consistently linked to the ms-3 gene at 5.2 cM. These markers were also present in 22 heterozygous fertile F1 plants having the ms-3 gene. The RAPD and SCAR markers linked to the ms-3 gene identified, and confirmed here could be utilized for backcrossing of male sterility into elite melon cultivars and lines for use as parents for F1 hybrid seed production.