The correct identification of species diversity of small single-celled green coccoid microalgae still causes difficulties, since their relatively simple morphology hides a high physiological, ecological and genetic diversity. The use of molecular genetic methods has revolutionized the study of the true biodiversity of so-called “small green balls,” allowing the discovery of numerous new taxa. This article presents the results of a study of strains recently isolated from small freshwater urbanized lakes (Vasilievsky Lakes system, Samara region, Russian Federation). Morphologically, these strains were close to the genus Meyerella: spherical cells, cup-shaped, or wide girdle-shaped parietal chloroplast without pyrenoid. Analysis of the 18S–ITS1–5.8S–ITS2 sequences also showed that the studied strains belong to this genus. Comparison of morphological characteristics, habitat and lifestyle, analysis of tree topology, genetic distances and secondary structures of the ITS1 and ITS2 spacers of the Meyerella members, as well as the delimitation results using the Automatic Barcode Gap Discovery (ABGD) method, the Poisson Tree Processes (PTP) model, the Generalized Mixed Yule The Coalescent (GMYC) method allowed us to establish that the studied strains ACSSI 346, ACSSI 362 and ACSSI 363 are representatives of a new species – M. similis sp. nov.