The taxonomy of alpine Primula species has long been in dispute because of high morphologic variability and several hybridisations. In Primula species, the trichome height and the colour of hair-tips are usually indicated as diacritic characters, but in our experience this is not adequate. The present study, focused on Primula auricula, Primula daonensis and Primula hirsuta, therefore proposes the use of other morphologic trichome parameters (size and dimensional ratio of stalk, neck and gland head). Phytochemical investigations about the flavonoid composition (epicuticular and vacuolar) of leaves, as taxonomic markers, have also been performed. We report the isolation and identification of two new flavonol glycosides, isorhamnetin 3-O-(2,6-di-O-beta-D-glucopyranosyl-beta-D-glucopyranoside) (1) and kaempferol 3-O-(2-O-alpha-L-rhamnopyranosyl-6-O-beta-D-xylopyranosyl-beta-D-glucopyranoside) (2) and of eight known flavonoids. Size and dimensional ratio of the three trichome elements (stalk, neck and glandular head) are typical for each species analysed. The flavonoid profile well characterise the entities under study. Three different profiles have been obtained with both vacuolar and epicuticular flavonoids. The morphologic and phytochemical markers proposed in this work seem to be parameters which significatively discriminate the species under study.