Soft rot disease is one of the primary issues in the production of colored calla lilies, significantly limiting large-scale production. This research conducts an in-depth investigation of the class III peroxidase gene family in colored calla lily, identifying 80 ZePER genes, with their motifs and structural domains remaining conserved. Through phylogenetic tree analysis, these genes were classified into 9 distinct clades. Collinearity analysis and the distribution of ZePER genes suggest that the two main events of ZePER gene family evolution was whole-genome duplication (WGD) as well as tandem duplication. Cis-acting element analysis showed that the ZePER genes could be directly modulated by essential hormones like jasmonic acid (JA) and salicylic acid (SA), highlighting their role in biotic stress responses. Transcriptome profiling revealed tissue-specific gene expressions and their essential function in responding to soft rot bacteria. Upon inoculation with Pectobacterium carotovorum, the leaves manifested a significant upregulation of ZePER genes expression, and there was a concurrent surge in JA and SA content. Treatments with methyl jasmonate (MeJA) and benzothiadiazole (BTH) induced ZePER gene expression and augmented the plant's disease resistance. This indicates the crucial role of ZePER genes in regulating reactive oxygen species in leaves. In summary, these findings emphasize the importance of ZePER genes in the defense mechanisms of colored calla lily.