Abstract: 【Objective】 This study aimed to estimate SNP genetic distances between pepper（Capsicum annuum L.） parents using genotyping-by-sequencing（GBS），and predict the heterosis of pungency-related traits in hybrid offspring through combining ability analysis，providing theoretical basis for the selection of parents and heterosis utilization in breeding new high-pungency varieties. 【Method】 A total of 30 hybrid combinations were generated using 11 pepper inbred lines（5 female parents，A1-A5，and 6 male parents，B1-B6）as parents in incomplete diallel cross（NCⅡ）mating design. Five pungency related traits，including dihydrocapsaicin，capsaicin，total capsaicin content，Scoville heat unit （SHU）and pungency degree were evaluated in both parents and hybrids. Correlations among SNP genetic distance，combining ability，and heterosis for each trait were analyzed. 【Result】 A total of 20.0 Gb of original data，with 19.9 Gb of clean reads，were obtained by Illumina sequencing. The average of Q20 was 97.3%，and the average GC content was 36.59%. Through comparison，a total of 1671621 SNP loci and 1732641 SNP variant loci were obtained. The genetic dis‐ tances between the 11 parents ranged from 0.0299 to 0.4762. Heterosis was commonly observed for pepper pungency related traits. The most obvious heterosis was observed in A5×B6 for dihydrocapsaicin，A5×B1 for capsaicin，and A5×B3 for total capsaicin content，SHU and pungency degree. General combining ability（GCA）effect values varied considerably among different pungency related traits of different parents. Among them，A5 exhibited high GCA effect values for capsaicin，and B6 for dihydrocapsaicin. The hybrid combinations A5×B6（dihydrocapsaicin）and A5×B1（capsaicin） showed the highest specific combining ability（SCA）effect values，suggesting that one of the parents with high GCA effect values contributed to high SCA effect values in their offspring. SCA showed an extremely significant positive correlation with heterosis for all pungency related traits（P<0.01，the same below），with correlation coefficients ranging from 0.466 to 0.782. However，GCA showed weak or negative correlations with heterosis. The heterosis for dihydrocapsaicin， total capsaicin content，SHU and pungency degree were significantly（P<0.05）or extremely significantly positively correlated with SNP genetic distance，with the correlation coefficients ranging from 0.382 to 0.579. 【Conclusion】 To predict heterosis for pungency related traits in pepper via SNP genetic distance and SCA is feasible，but GCA should also be considered. Therefore，when predicting heterosis for pungency related traits in hybrid combinations，combining ability and genetic distance can be used together to develop higher-pungency hybrid combinations.