Abstract <p>The effectiveness of cryopreservation of cyanobacteria and eukaryotic microalgae from various taxonomic groups, including charophytes, chlorophytes, and heterokontophytes, was evaluated for 24 strains from the funds of the All-Russian Collection of Microorganisms (VKM). This comparative study was conducted on the cultures of microalgae that differ in cellular size, morphological organization of the thallus, method of reproduction, presence and size of mucilage envelopes, and the ability to form dormant cells. Two variants of cryoprotective agents (methanol and dimethyl sulfoxide), two types of nutrient media (slant agar and liquid medium), as well as three methods for determining the post-cryopreservation survival rates of microalgae were tested. A two-stage cryopreservation protocol that employed both cryoprotective agents (methanol and dimethyl sulfoxide) was successfully applied to all 24 strains studied, regardless of their taxonomic affiliation and morphological characteristics. Based on the obtained results, we developed a standard procedure for cryopreservation of microalgae and cyanobacteria that included a liquid culture medium with dimethyl sulfoxide, as well as two methods for determining the survival of organisms after cryopreservation, growth in a liquid medium and streaks on agar. The proposed protocol ensures not only the preservation of cell viability and the possibility of further use of a strain as a morphologically and genetically representative sample, but also minimizes the time and resource costs, as well as the risk of culture contamination.</p>