Aconitum lasiocarpum (Carpathian endemic) and A. variegatum (European endemic) occur sympatrically in the Polish Western Carpathians. Here their taxonomic hybrid A. ×pawlowskii occurs. The aim of this study was to determine the relationship between the taxonomic (Linnaean approach) and genetic structure (PCR-ISSR analysis) of the populations and individuals in two allopatric and four sympatric populations. We determined 309 individuals (OTUs) to species, subspecies and nothospecies using the Linnaean system of classification, and then genetically fingerprinted 39 randomly chosen OTUs. Comparison of the Nei and Li distances obtained from ISSR and morphological matrices using the Mantel test indicated a significant correlation (n = 39, r = 0.53, P = 0.001). Genetic analysis (NEWHYBRIDS) pointed to 7 OTUs as being later-generation hybrids (B1 introgessants) in the sympatric area. Five of them belong to A. variegatum, indicating cryptic introgression, and two belong to A. ×pawlowskii. Nonmetric multidimensional scaling (NDMS) showed gene flow between A. lasiocarpum and A. ×pawlowskii. Allopatric, morphologically pure A. lasiocarpum and A. variegatum populations differed significantly in their ISSR profiles (Fischer's R×C test, P < 0.0001). Expected heterozygosity (Hj) was significantly (p=0.05) lower in allopatric (0.1261-0.1268) than in sympatric populations (0.1348-0.1509), indicating a genetic melting pot in sympatry. The results support the existence of a natural interspecific hybrid swarm zone in the sympatric area of occurrence of Aconitum, and the taxonomic circumscription of the nothospecies within the Linnaean taxonomic system