The chili pepper (Capsicum) is both an important spice and fresh vegetable worldwide. C. baccatum is a lesser known domesticated species that is native to the Andean region. Fruit traits such as color, shape, and pungency markedly vary in this species. C. baccatum has potential as a bioresource for future chili pepper breeding programs. Although extensive studies have been conducted on the pungency of C. annuum, that of C. baccatum has not been examined in as much detail. In the present study, capsaicinoid contents were analyzed in 36 C. baccatum accessions. Capsaicinoid contents ranged between 0 and 4,258 μg/gDW. Furthermore, a negative relationship was observed between capsaicinoid contents and fruit weights. Although the pungency of C. baccatum is regarded as low-mild, very few non-pungent accessions were detected ; only one non-pungent accession (‘Kaleidoscope’) was identified among the C. baccatum accessions examined. In order to validate the stability of non-pungency in the accession, capsaicinoid contents were determined at different harvest dates, along with other accessions with different pungencies. Although capsaicinoid contents in other C. baccatum accessions changed with the picking date, capsaicinoid was not detected in ‘Kaleidoscope’ at any date. The non-pungent accession reported here may be useful for future C. baccatum pepper breeding programs.