The recent identification of saxitoxin-producing Scytonema cf. crispum triggered a survey of metaphyton and periphyton for Scytonema spp. in 34 high-use recreational lakes across Canterbury, New Zealand. Scytonema was observed in 10 of the lakes surveyed. Three morphospecies were identified: Scytonema cf. crispum, Scytonema cf. chiastum and Scytonema cf.fritschii. Environmental samples containing Scytonema were analysed for saxitoxins using the Jellett rapid test for paralytic shellfish poisoning, and saxitoxin variants were identified in positive samples using high-performance liquid chromatography with fluorescence detection (HPLC-FD). Cultures were established from selected sites and their phylogeny investigated using partial 16S rRNA gene sequences. These cultures were also screened for a region of sxtA, a gene involved in saxitoxin production. Cultures containing the sxtA gene were analysed for saxitoxins with HPLC-FD. Saxitoxins were only identified in cultures of S. cf. crispum and environmental samples containing this species. HPLC-FD analysis of these environmental samples and cultures identified saxitoxin and the variants gonyautoxins (GTX1-5), neosaxitoxin, decarbamoyl saxitoxin and decarbamoyl gonyautoxins (dcGTX2/3). This was the first report of these saxitoxin variants from cyanobacteria in New Zealand. All cultures of S. cf. crispum contained the sxtA gene segment. The partial 16S rRNA gene sequence of Scytonema C. Agardh ex Bornet & Flahault cultures were compared with cyanobacterial sequences from GenBank, only S. cf.fritschii clustered amongst other Scytonema species. The identification of metaphytic saxitoxin-producing S. cf. crispum highlighted a new freshwater habitat where toxic cyanobacteria may need to be monitored.