A new species from Vietnam, Cryptomonas vietnamica sp. nov., is described based on morphological and molecular data. Six strains from different habitats were analyzed. Cryptomonas vietnamica is characterized by large cells up to 54 µm long, 30 µm wide and 20 µm thick, flattened in dorso-ventral plane and often twisted. Phylogenetic relationships inferred from nuclear small and large subunit ribosomal DNA sequences show that the new species forms a clade with Cryptomonas lundii, a rare taxon, described from Europe. Cryptomonas lundii is reported for the first time from Russia and second time since its initial description.