We investigated twenty-six strains of Xanthidium antilopaeum Kütz. and seven strains of X. cristatum Ralfs isolated from various European localities or obtained from public culture collections. A combination of molecular, geometric morphometric, and morphological data were used to reveal the patterns of the phylogenetic and morphological differentiation of these taxonomically very compli-cated desmid taxa. The molecular data based on trnGucc and ITS rDNA sequences illustrated the monophyly of both the complexes, which indicated that their traditional morphology-based discriminative criteria, such as the different number of spines, may generally continue to be considered relevant. The single exception was X. antilopaeum var. basiornatum B. Eichler et Raciborski, which was positioned outside the X. antilopaeum/cristatum clade. The independent status of this taxon was also confirmed on the basis of the geometric morphometric data, so that we concluded that it probably represents a separate species. Within X. cristatum complex, the traditional varieties X. cristatum var. cristatum Ralfs, X. cristatum var. uncinatum Ralfs, and X. cristatum var. scrobiculatum Scott et Grönblad turned out to be separate taxa. Conversely, X. cristatum var. bituberculatum Lowe lacked any taxonomical value. Our data on X. antilopaeum illustrated extensive phylogenetic as well as phenotypic variability within this species complex. However, our data did not result in any unambiguous pattern that would allow sound taxonomic classification. Finally, we also found out that the morphologically peculiar Staurastrum tumidum Ralfs belongs to the genus Xanthidium based on the combined rbcL + cox III data set. Consequently, this species was formally transferred to this genus.