Variability within eight cpDNA introns including trnS-trnfM, trnL-trnT, trnH-psbA, trnF-trnL, trnD-trnT, trnCrpoB,
rps16 and matK, and the nuclear waxy introns was examined in seven species of Capsicum (C. annuum, C.
baccatum, C. chinense, C. frutescens, C. pubescens, C. chacoense and C. rhomboideum) in order to evaluate the
feasibility of utilizing these loci for DNA barcoding within the C. annuum complex. Numerous insertions/deletions
(indels) and substitutions were detected in all cpDNA introns. However, none was sufficient to differentiate the individual
members of the C. annuum complex (C. annuum, C. chinense and C. frutescens). Variation within trnL-trnT, trnF-trnL
and trnH-psbA enabled the differentiation of the complex from the other taxa examined. In contrast, single base indels and
substitutions within the waxy introns permitted the differentiation of all taxa within the plant materials examined. The use
of trnH-psbA or trnL-trnT, and the waxy introns is proposed for barcoding members of the C. annuum complex.