Bacterial spot caused byXanthomonas euvesicatoriais a major disease of pepper (Capsicum annuumL.) in warm and humid production environments. Use of genetically resistant cultivars is an effective approach to manage bacterial spot. Two recessive resistance genes,bs5andbs6, confer non-race-specific resistance against bacterial spot. The objective of our study was to map these two loci in the pepper genome. We used a genotyping-by-sequencing approach to initially map the position of the two resistances. Segregating populations forbs5andbs6were developed by crossing susceptible Early CalWonder (ECW) with near-isogenic lines ECW50R (bs5introgression) or ECW60R (bs6introgression). Following fine-mapping,bs5was delimited to a ~535 Kbp interval on chromosome 3, andbs6to a ~666 Kbp interval in chromosome 6. We identified 14 and 8 candidate resistance genes forbs5andbs6, respectively, based on predicted protein coding polymorphisms between ECW and the corresponding resistant parent. This research enhances marker-assisted selection ofbs5andbs6in breeding programs and is a crucial step towards elucidating the molecular mechanisms underlying the resistances.