Maintaining pure cultures using preservation methods is of high importance for biotechnological purposes. However, preservation does not necessarily guarantee the genetic stability of these cultures. Therefore, preservation methods are currently needed to assure viability as well as genetic, physiological, and morphological integrity across storage periods. In this study, preservation of five isolates from the microalgae and cyanobacteria collection of the Plant Biology Department, Federal University of Viçosa, Minas Gerais, Brazil was investigated via monthly analyses of cell viability, biomass recovery, and contaminant concentrations over a period of 120 days. Lyophilization was adequate for both heterocystous cyanobacteria and other strains that were able to differentiate hormogones or to synthesize thick layers of exopolysaccharides. Lyophilization was also able to maintain cultures with low levels of contaminants. Dimethyl sulfoxide was relatively efficient, though some of the strains were susceptible to its cytotoxic effects. Our results demonstrated that cryopreservation with glycerol was the most efficient method. The ability to routinely preserve cyanobacterial strains reduces costs associated with maintaining large culture collections and reduces the risks of losing particular strains or species through contamination and genetic drift. The results obtained in this study are therefore discussed in the context of the efficiency of the methods and the current need to develop suitable methods for maintenance of cyanobacterial collections.