A proposal for chemical characterisation and quality evaluation of botanical raw materials by analysing the glandular trichomes from the leaves of two different populations of yacón (Polymnia sonchifolia Poeppig & Endlicher, Asteraceae) is described. This species is an Andean medicinal plant and the tea prepared with their leaves displays hypoglycemic property. The method was based on the glandular trichome microsampling using LC/DAD. Qualitative chromatographic fingerprints of the glands were obtained by isocratic runs and then compared between the two populations, showing the same qualitative profile. The two main metabolites detected in the glands were later isolated from a leaf rinse extract by preparative separation and identified as the melampolides enhydrin and uvedalin. These compounds, subtypes of sesquiterpene lactones, were used as chemical markers. This technique is applicable to other medicinal plants and can be used for the evaluation of the quality of dried material or leaf rinse extracts.