Gummy stem blight is one of the major diseases affecting watermelon production. The discovery and utilization of resistance genes against gummy stem blight are of great significance for the innovation of disease-resistant watermelon germplasm and the breeding of resistant watermelon varieties. In this study, a recombinant inbred line (RIL) population derived from a cross between the gummy stem blight-resistant variety germplasm PI189225 and the susceptible variety germplasm K3 was used as experimental materials. Bulked segregant analysis (BSA) combined with whole-genome resequencing was performed on the parental lines and resistant/susceptible pools to identify candidate genomic regions associated with gummy stem blight resistance. Additionally, transcriptome sequencing (RNA-seq) data were integrated to mine candidate genes through association analysis. The results showed that BSA-seq analysis identified genome candidate regions significantly associated with watermelon gummy stem blight resistance were identified on chromosome 5 and chromosome 10 of watermelon, with a total length of 8.18 Mb, encompassing 681 genes. Functional analysis revealed that these genes are primarily involved in biological processes such as the brassinosteroid (BR) signaling pathway and the plant-pathogen interaction pathway. Through InDel markers and recombinant plant analysis, the watermelon gummy stem blight resistance interval was narrowed down to between markers Chr10_30103333 and Chr10_32554279 on chromosome 10, with an interval size of 2.45 Mb. Combined with differentially expressed genes in watermelon responding to gummy stem blight pathogen infection, By integrating transcriptome data related to gummy stem blight resistance, sixeven candidate genes were ultimately identified on chromosome 10. qRT-PCR analysis demonstrated that the expression of all sixeven candidate genes was induced by gummy stem blight pathogen infection. Among them, Cla97C10G194300, Cla97C10G200140195980 and Cla97C10G202140199290 were highly expressed in susceptible materials, whereas Cla97C10G200100, Cla97C10G201690, Cla97C10G202570, and Cla97C10G201940Cla97C10G195320, Cla97C10G196460, Cla97C10G198780 and Cla97C10G205250 exhibited high expression in resistant materials. The findings of this study provide an important theoretical basis and gene resources for molecular marker-assisted selection and the breeding of gummy stem blight resistant watermelon varieties.