A chemical and biological screening of 25 species of the Gentianaceae family has been undertaken. Both methanolic and dichloromethane extracts of Swertia calycina exhibited a strong antifungal activity against Cladosporium cucumerinum and Candida albicans. The compound responsible for this activity has been isolated and identified as 2-methoxy-1,4-naphthoquinone. It is the first naphthoquinone to be described in Gentianaceae species. LC-UV and LC-TSP-MS analysis of the crude extracts of Swertia calycina also allowed on-line identification of six known xanthones and secoiridoids.