The reliability of diarylheptanoids as chemotaxonomic markers at inter- and intraspecific levels has been investigated. Six diarylheptanoids were quantified in bark ethanol extracts of fourAlnusspp. populations by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The populations described here aslocus classicus Alnus glutinosa(I) andlocus classicus Alnus incana(III) are clearly differentiated. Compared to population I, individuals in population III have higher extract yields and hirsutanonol-5-O-β-D-glucopyranoside content and lower contents of hirsutanonol, rubranoside A and oregonin. Individuals from neighboring populations ofA. glutinosa(II) andA. incana(IV) share similar contents of hirsutanonol. All the studied populations exhibit a high intrapopulation variability of the selected diarylheptanoids; they have a heterogeneous chemotype and they partially overlap. The geographical proximity of populations II and IV increases their chemical similarity. Principal component analysis (PCA) clearly shows that the biggest dispersion of individuals lies within population IV. The reason for its heterogeneity might be its physical proximity to population II, i.e. the appearance of hybrids. Also, geometric morphometrics of leaves was performed as a screening criterion for spontaneous hybrids.