Genic male sterility (GMS) is an important trait for watermelon breeding programs to produce F1 hybrids without the laborious steps of emasculation and hand pollination; however, the inheritance of GMS and the underlying molecular mechanisms remain unclear. Here, we aimed to identify the causal genomic region for GMS in watermelon and develop single nucleotide polymorphism (SNP) markers linked to the trait. Two inbred lines harboring a male sterility gene were crossed to generate F2 and near-isogenic line (NIL) populations for mapping loci and evaluating SNP markers. Our study showed that the inheritance of GMS was controlled by a single recessive gene following Mendelian inheritance models in the segregation population. We applied bulked segregant analysis (BSA) and Illumina whole-genome resequencing (BSA-seq) to identify a candidate causal genomic region for GMS at 8.9–13.0 Mb on chromosome (Chr.) 6. Next, we selected seven high-resolution melting (HRM) markers by retrieving 1-Mb genomic sequences around SNPs located within the causal genomic region. The identified polymorphic SNPs were tested via HRM analysis in the F2 population. By further narrowing the putative causal region, we identified a deleted and frameshifted gene, Cla97C06G117840, at Chr. 6. As a result, we developed allele-specific PCR and HRM markers, which completely cosegregated with the male-sterility phenotype of the F2 and NIL populations. Overall, our results will help effectively use GMS in watermelon breeding programs and accelerate the production process of F1 hybrids.