Male sterility is used to mass-produce F₁ hybrid seeds in pepper (Capsicum annuum L.). In particular, the development of genetic male sterility (GMS)-linked molecular markers may play a crucial role in hybrid breeding of pepper. To date, approximately 20 GMS genes have been identified in pepper. Among these, several molecular markers for the ms₃ gene have been developed in previous studies; however, they are not completely linked and thus have limitations for use in selection. Therefore, in the present study, we aimed to develop molecular markers for ms₃ selection using single-nucleotide polymorphism (SNP)-based high-resolution melting (HRM) analysis. Chi-square test was conducted using three F₂ segregating populations, and the results confirmed a 3:1 segregation ratio between male-fertile and male-sterile plants. A total of 128 primer sets were designed by selecting SNPs near the ms₃ gene, and 25 HRM markers were successfully developed. Using 420 individuals from the F₂ segregating population ‘GMS3,’ a high-density genetic linkage map of pepper chromosome 1 was constructed, with eight HRM markers found to be co-segregated with the ms₃ gene. Subsequent experiments using various plant materials validated these eight markers, ultimately identifying two HRM markers, HRM119655681 and HRM135273656, for the final selection. These two markers showed co-segregation between the phenotype and genotype of ms₃ across all plant materials used in the study. The markers developed in this study are expected to be effective for maternal line development and large-scale F₁ hybrid seed production using ms₃ in pepper.