Six coding genes of SEPALLATA(SEP) subfamily members were identified through genome-wide analysis of the ST-8 Zhangshugang pepper. The physicochemical properties, chromosome localization, encoded protein conserved motifs and conserved structures of the subfamily members were analyzed. The phylogenetic tree was constructed with the SEP genes of pepper, Arabidopsis, tomato, rice and maize. Furthermore, tissue expression level of CaSEP3 and subcellular localization of encoded protein were explored. The results showed that SEP genes of pepper were distributed on five chromosomes, with all their encoded protein contained MADS domain(MADS_MEF2_like) and K-box domain. SEP genes could be divided into two branches: SEP3 and SEP1/2/4, which was similar to the evolutionary development of tomato and Arabidopsis. CaSEP3 was a homologous protein of AtSEP3, which was localized in the nucleus. CaSEP3 was highly expressed in flower buds, placenta and pericarp, which was speculated to be involved in development of flower and fleshy fruit in pepper. After common hormone and abiotic stress treatments(0~24 h), the expression of CaSEP3 was up-regulated by ABA, H2O2 and NaCl, while the expression of CaSEP3 in leaves and roots did not change significantly under other treatments.