Capsicum chinense is a domesticated hot pepper species in the Capsicum genus that originated in the Amazon and is consumed in USA, the Caribbean and South America. Although a characteristic of this species is high pungency, some non-pungent or lowpungent strains, called ''Aji Dulce'' (sweet pepper in Spanish), exist in the Caribbean region. In the present study, low-pungent C. chinense accessions were analyzed in order to elucidate the genetic mechanisms responsible for low pungency. All low-pungent C. chinense accessions in this study carried non-functional alleles of putative aminotransferase (pAMT), which catalyzes the formation of vanillylamine from vanillin in the capsaicinoid biosynthetic pathway. These low-pungent accessions produced capsinoids, low-pungent capsaicinoid analogs. The pamt mutation in each strain was characterized using allele-specific markers, and one novel pamt allele (pamt 7 ) was identified. The pamt 7 had a new hAT family transposon insertion in the second exon region, which caused the loss of pAMT expression. pamt 7 is apparently an ancestral allele for pamt 6 because the 7-bp insertion in pamt 6 can be regarded as a footprint of the transposon. A phylogenetic analysis of pamt alleles was performed to examine their relationships. Combined with previously reported pamt alleles, the Tcc family transposon insertion and its excision were involved in the generation of various pamt alleles in C. chinense. A phylogenetic analysis of pamt alleles showed that at least five occurred within C. chinense after speciation of the Capsicum genus. In conclusion, the results of the present study identified pamt as the main and most frequent gene controlling low pungency in C. chinense. Allelic variations in loss-of function pamt and their wide distribution demonstrated the potential of C. chinense bioresources for genetic improvements to pungency and metabolic profiles in hot pepper breeding programs.