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The purpose of A Guide to the Identification of Common Blue-Green Algae (Cyanoprokaryotes) in Australian Freshwaters is to provide keys to the morphological identification of the reported genera of cyanoprokaryotes in Australia (both planktonic and benthic) and to facilitate the identification of the common taxa associated with freshwater blooms and the impairment of water quality. A Guide to the Identification of Common Blue-Green Algae (Cyanoprokaryotes) in Australian Freshwaters does not attempt to provide an identification to all reported taxa in Australia. The approach taken is to present keys, photographic images and illustrations of those taxa which are known or have potential to impair water quality and is intended primarily as a practical guide to those involved in water quality monitoring and research. For the first time, descriptions are provided in a single document for cyanoprokaryote taxa occurring in both temperate and sub-tropical climatic regions of Australia.