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Using genetic markers 18S V4 rDNA and rbcL and morphological investigation of the diatom genus Placoneis, we described three new species. The new species, Placoneis baikaloelginensis sp. nov., Placoneis subundulata sp. nov., Placoneis neohambergii sp. nov. were isolated from Russia (Lake Baikal) and Vietnam (waterbodies of Cát Tiên National Park (Đồng Nai Province) and Khánh Hòa Province). We examine relationships within the Cymbellales and show that the genera Placoneis, Paraplaconeis and Geissleria are phylogenetically independent. We discuss the importance of careful identification of strains used for phylogenetic analysis and we show the history of identification of several different Placoneis elginensis strains. After careful identification of Placoneis elginensis vouchers, we found that we have a few independent species. The question of cryptic or pseudocryptic species in this context is discussed.