‘No.80’ (Capsicum chinense) from the Caribbean is a valuable genetic source from the aspect of its non-pungent and highly aromatic traits. In the present study, the non-pungency, volatile components, and phylogenetic origin of ‘No.80’ were analyzed with another C. chinense cultivar, ‘No.2’ from Brazil, which is also non-pungent but less aromatic. Expressions and deduced amino acid sequences of acyltransferase (Pun1) of ‘No.80’ and ‘No.2’ were normal compared with a pungent cultivar, ‘Habanero’. Insertions of 7-bp and 8-bp resulting in frameshift mutations were found in the coding regions of putative aminotransferase (p-AMT) of ‘No.80’ and ‘No.2’, respectively. Co-segregation of these insertions with the non-pungent phenotypes in F1 and F2 populations obtained from crossing ‘No.80’ or ‘No.2’ with ‘Habanero’ suggested that non-pungency in these cultivars arose from genetic mutations of p-AMT that occurred independently. Moreover, molecular phylogenetic analysis suggested that ‘No.80’, a close relative of ‘No.2’, originates from capsicums migrated from the South American mainland. In addition to pungency, we assessed the volatile components of the highly aromatic ‘No.80’, the less aromatic ‘No.2’, and their F1 hybrid using gas chromatography. ‘No.80’ contained higher levels of aroma-contributing volatiles than ‘No.2’, which correlated with the stronger and weaker aromas of two cultivars. Further, the fruit of F1 progenies emitted a number of volatile compounds between or higher than their corresponding parents. Based on these results, the approaches for breeding highly aromatic non-pungent cultivars are discussed.