| Summary: | Amomi Fructus is widely used to treat digestive disorders, and <i>Amomum villosum</i>, <i>A. villosum</i> var. <i>xanthioides</i>, and<i> A. longiligulare</i> are permitted medicinally in national pharmacopeias. However, there are a variety of adulterants present in herbal markets owing to their morphological similarities to the genuine <i>Amomum </i>species. Forty-two Amomi Fructus samples from various origins were identified using internal transcribed spacer and chloroplast barcoding analyses, and then their chromatographic profiles were compared using chemometric analysis for chemotaxonomic monitoring. Among the Amomi Fructus samples, <i>A. villosum</i>, <i>A. longiligulare</i>, <i>A. ghaticum</i>, and <i>A. microcarpum</i> were confirmed as single <i>Amomum</i> species, whereas a mixture of either these <i>Amomum</i> species or with another <i>Amomum</i> species was observed in 15 samples. Chemotaxonomic monitoring results demonstrated that two medicinal <i>Amomum </i>samples, <i>A. villosum</i> and <i>A. longiligulare</i>, were not clearly distinguished from each other, but were apparently separated from other non-medicinal <i>Amomum</i> adulterants. <i>A. ghaticum</i> and <i>A. microcarpum</i> samples were also chemically different from other samples and formed their own species groups. <i>Amomum </i>species mixtures showed diverse variations of chemical correlations according to constituent <i>Amomum</i> species. Genetic authentication-based chemotaxonomic monitoring methods are helpful in classifying Amomi Fructus samples by their original species and to distinguish genuine <i>Amomum</i> species from the adulterants.
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