ATP-binding cassette (ABC) transporter genes act as transporters for different molecules across biological membranes and are involved in a diverse range of biological processes. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC transporter proteins in three
Capsicum
species, i.e.,
Capsicum annuum
,
Capsicum baccatum
and
Capsicum chinense
.
Capsicum
is a valuable horticultural crop worldwide as an important constituent of many foods while containing several medicinal compounds including capsaicin and dihydrocapsaicin. Our results identified the presence of a total of 200, 185 and 187 ABC transporter genes in
C
.
annuum
,
C
.
baccatum
and
C
.
chinense
genomes, respectively. Capsaicin and dihydrocapsaicin content were determined in green pepper fruits (16 dpa). Additionally, we conducted different bioinformatics analyses including ABC genes classification, gene chromosomal location,
Cis
elements, conserved motifs identification and gene ontology classification, as well as profile expression of selected genes. Based on phylogenetic analysis and domain organization, the
Capsicum
ABC gene family was grouped into eight subfamilies. Among them, members within the ABCG, ABCB and ABCC subfamilies were the most abundant, while ABCD and ABCE subfamilies were less abundant throughout all species. ABC members within the same subfamily showed similar motif composition. Furthermore, common
cis
-elements involved in the transcriptional regulation were also identified in the promoter regions of all
Capsicum
ABC genes. Gene expression data from RNAseq and reverse transcription-semi-quantitative PCR analysis revealed development-specific stage expression profiles in placenta tissues. It suggests that ABC transporters, specifically the ABCC and ABCG subfamilies, may be playing important roles in the transport of secondary metabolites such as capsaicin and dihydrocapsaicin to the placenta vacuoles, effecting on their content in pepper fruits. Our results provide a more comprehensive understanding of ABC transporter gene family in different
Capsicum
species while allowing the identification of important candidate genes related to capsaicin content for subsequent functional validation.