MADS domain transcription factors play roles throughout the whole lifecycle of plants from seeding to flowering and fruit-bearing. However, systematic research into MADS-box genes of the economically important vegetable crop pepper (Capsicum spp.) is still lacking. We identified 174, 207, and 72 MADS-box genes from the genomes of C. annuum, C. baccatum and C. chinense, respectively. These 453 MADS-box genes were divided into type I (Mα, Mβ, Mγ) and type II (MIKC* and MIKCC) based on their phylogenetic relationships. Collinearity analysis identified 144 paralogous genes and 195 orthologous genes in the three pepper species, and 70, 114, and 10 MADS-box genes specific to C. annuum, C. baccatum and C. chinense, respectively. Comparative genomic analysis highlighted functional differentiation among homologous MADS-box genes during pepper evolution. Tissue expression analysis revealed three main expression patterns: highly expressed in roots, stems, leaves and flowers (CaMADS93/CbMADS35/CcMADS58); only expressed in roots; and specifically expressed in flowers (CaMADS26/CbMADS31/CcMADS11). This study provides the basis for an in-depth study of the evolutionary features and biological functions of pepper MADS-box genes.