In our chemotaxonomic investigation of pharmaceutically relevant Crataegus species, the qualitative and quantitative flavonoid fingerprint of Crataegus monogyna and C. pentagyna is presented. Six flavonoids were identified as vitexin-2''-O-rhamnoside (1), vitexin (2), isovitexin (3), rutin (4), hyperoside (5), and isoquercitrin (6). Besides the verification of the main compounds isoorientin (7) and orientin (8) in C. pentagyna, further four flavonoids were isolated and identified as isoorientin-2''-O-rhamnoside (9), orientin-2''-O-rhamnoside (10), isovitexin-2''-O-rhamnoside (11), and 8-methoxykaempferol-3-O-glucoside (12) by means of 1D- and 2D-NMR, MS, and UV analyses. Compound 12 was isolated for the first time from C. pentagyna. In contrast to C. pentagyna, C. monogyna samples were predominated by 4'''-acetylvitexin-2''-O-rhamnoside (13), which was missing in C. pentagyna. Hence, 13 represents an interesting compound for chemotaxonomy of C. monogyna, whereas the main flavonoids 7, 8, and 12 could be proposed as markers for C. pentagyna. The absence of 7, 8, 12, and 13 in C. laevigata offers an appropriate tool for additional differentiation from C. monogyna and C. pentagyna, and for sample identification and quality control of the three main Crataegus species used in European phytotherapy.