Similarity and diversity of the phenotype and nucleotide sequences of certain genome loci among the single-celled microalgae isolated from White Sea benthic invertebrates were studied to extend the knowledge of oxygenic photoautotrophs forming microbial communities associated with animals. We compared four Desmodesmus isolates (1Hp86E-2, 1Pm66B, 3Dp86E-1, 2Cl66E) from the sponge Halichondria panicea, trochophore larvae of the polychaete Phyllodoce maculata, and the hydroids Dynamena pumila and Coryne lovenii, respectively. The microalgae appeared to be very similar featuring the phenotypic and genetic traits characteristics of unicellular representatives of the genus Desmodesmus. At the same time, isolates from different animal species displayed certain differences in (i) the epistructure morphology; (ii) type and number of the inclusions such as interthylakoid starch grains and cytoplasmic oil bodies and (iii) fatty acid composition; in Desmodesmus sp. 1Hp86E-2, these differences were most pronounced. Phylogenetic analysis based on ITS1-5.8S rRNA-ITS2 and rbcL sequences showed that all isolates studied differ from known classified representatives of Desmodesmus combining a deletion in the conservative 5.8S rRNA gene and long AC-microsatellite repeats in the ITS1 whereas 1Hp86E-2 represented a distinct branch within this group.