Hot pepper (Capsicum annuum L.) is one of the most important vegetable crops in China, but floods bring substantial decreases in production over the past several decades. In order to investigate the mechanisms of waterlogging resistance in mutant hot pepper, we measured the agronomic traits of mutant and wild-type, as well as the activities of root antioxidant enzymes and the contents of osmotic regulation substance. At the same time, we did transcriptome sequencing on the plant roots, and screened for differentially expressed genes between mutant and wild-type. The results showed that, under waterlogging stress, the mutants could grow normally, and the activities of their superoxide dismutase, peroxidase, catalase, and glutathione reductase were significantly increased, as well as the contents of proline and soluble sugar. The accumulation of malondialdehyde and hydroxyl radical in mutants was significantly reduced. Among the 61 differentially expressed genes from transcriptome analysis, 24 genes were up-regulated and 37 genes were down-regulated in mutants. After functional analysis, we found 8 genes related to the metabolism of endogenous hormone and protective enzymes, among which, auxin-induced protein related gene cap.ARATH, ethylene response related gene Cap.RAP2, MYB family related gene Cap.MYB1R1, and the 4 genes related to peroxidase Cap. POD, were significantly up-regulated in mutants, while the Capana01g001329 gene was down-regulated. These results suggest that under waterlogging stress, the mutant could enhance its resistance to waterlogging by regulating the genes involved in metabolism of endogenous hormones and protective enzymes. This study provides the scientific basis for elucidating the gene regulation network of mutant pepper under waterlogging stress.