Isolation, cultivation and identification of Spirogyra morphotypes are fundamentals for a continued study on its infra- and interspecific relationships. The monographs published by Czurda (1932), Kolkwitz and Krieger (1941), Transeau (1951), Randhawa (1959) or Kadlubowska (1984) are based solely on morphological diacritical features of field collected material. However, Allen (1958) was the first to observe polyploidy in clonal cultures and therefore introduced the term “species complex” for derived groups with euploidal diffences and distinct morphology leading to multiple “traditional” species. A “species complex” in Spirogyra consists of a series of morphotypes of different ploidy emanating from a clonal morphotype. Hoshaw et al. (1985, 1987) confirmed polyploidy in Spirogyra and McCourt and Hoshaw (1990) focused on problems associated with species concepts in this genus. Richard et al. (1990) confirmed that polyploidy plays a major role in morphological diversity of Spirogyra filaments. Recently, cytological study of Kim et al. (2009) underlined the aneuploidy phenomenon in the genus. Summing up, the uncertain position of Spirogyra within the Zygnemataceae and its complex species structure can be resolved only by detailed studies of clonal cultures including traditional characters, karyology (Kim et al. 2009) and molecular markers as provided in this study. Knowledge of nuclear cytology in algae remains to be much improved, compared to that in higher plants and animals. We supposed that additional species complexes will be delimited and that polyploidy is widespread among Spirogyra. Special attention was paid to the different karyological methods.