A culture collection of freshwater planktonic and benthic cyanobacteria collected from sites across New Zealand has been established at the Cawthron Institute, Nelson, New Zealand. Limited resources led to uncertainty regarding the long-term maintenance of this collection. The present study demonstrates cryopreservation to be a viable method for long-term storage of cyanobacteria. Seventeen of 20 strains evaluated were successfully cryopreserved using the permeating cryopreservation agent dimethyl sulfoxide (Me2 SO), at a final concentration of 15% (v/v). Cyanotoxin analysis was undertaken on selected strains known to produce microcystins, nodularin, anatoxin-a, and saxitoxins. All strains retained their ability to produce these toxins following cryopreservation.