Three different pollination syndromes (bee, hummingbird and moth-pollination syndromes) have been described for the different species of the genus Schizanthus Ruiz & Pav. (Solanaceae). Two closely related species from a phylogenetic point of view, Schizanthus grahamii and Schizanthus hookeri, show hummingbird and bee-pollination syndromes, respectively. One of the traits used to assign these pollination syndromes is the colour of the petals, which is red in S. grahamii and bluish-pink in S. hookeri. The objective of this work was to establish the differences in the anthocyanin composition of these two Schizanthus species that contribute to the different pollination syndrome. Identification of the pigments was carried out from the chromatographic and spectral data supplied by the HPLC-DAD-MSn analyses of the samples. Alkaline and acid hydrolyses were also performed in the extracts and in some isolated compounds in order to confirm the identities. First difference between these two species was found in the total anthocyanin content, which was about 13-fold higher in S. grahamii than in S. hookeri. Furthermore, the major peak was also different in both cases, thus explaining quantitative and qualitative colour differences between species. Delphinidin 3-O-rutinoside represented ca. 72% of the total area in S. grahamii and petanin (Petunidin 3-O-p-coumaroylrutinoside-5-O-glucoside) accounted for almost 62% of the total area in S. hookeri. The presence of the p-coumaroylrutinosyl moiety in the petanin makes the intramolecular copigmentation possible, thus conferring the bluish-pink hue to the petals of S. hookeri. Delphinidin 3- O-rutinoside is in turn responsible for the red colour exhibited by the petals of S. grahamii and along with other floral traits, responsible for the attraction of hummingbirds to the plant. Pigments structurally related to petanin, which have been often detected in other genus of Solanaceae, were detected in both species and in similar contents, supporting results from previous studies that pointed to a bee-pollinated common ancestor for both species that further specialised acquiring traits attractive to hummingbirds and among them, red colour of the petals which is mainly supplied by delphinidin 3-O-rutinoside.