| Summary: | <i>Fragilaria</i> and <i>Ulnaria</i> are two closely related diatom genera for which the delimitation and circumscription of several species is unclear. We studied strains isolated from Lake Baikal and compared them with the species from freshwater reservoirs in Europe and Asia using phylogenetic and species delimitation methods, microscopy and interclonal crossing experiments. The results of the phylogenetic analyses of the fragments of <i>rbc</i>L and 18S rRNA genes revealed that baikalian <i>F. radians</i> clade was independent from the representatives of the genus from other localities. Among <i>Ulnaria</i> we found the following 18S rRNA phylogenetic tree groups at species level: <i>U. acus</i>, <i>U. ulna</i> and <i>U. danica</i>. Genetic distance between genera varied between 3.9–10.2% substitutions in <i>rbc</i>L gene and 3.2–11.5% in 18S rRNA. The boundary between intraspecies and interspecies polymorphism for studied species of <i>Ulnaria</i> and <i>Fragilaria</i> in these marker genes was around 0.8% substitutions. Morphometric characters of individual strains showed their variability and division into <i>F. radians, U. acus</i> and <i>U. ulna</i> together with <i>U. danica</i>. Strains of <i>U. acus</i> and <i>U. danica</i> from different localities of Europe and Asia were sexually compatible inside the species. Sexual reproduction has never been observed in monoclonal cultures, either between this species or with strains of the <i>Fragilaria.</i>
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