Lake Omapere, Northland, New Zealand, contributes significant inputs of freshwater to Hokianga Harbour, and is subject to toxic cyanobacterial blooms. During summer 2004, ADDA-ELISA analysis indicated microcystins were present in Pacific oysters (Crassostrea gigas) in Hokianga Harbour, leading to farm closures. Once the bloom had abated, continued detection of low microcystin levels suggested toxin production may be from cyanobacteria in the harbour not the lake. In this study, 20 cyanobacterial strains were isolated from Lake Omapere, its outflow and Hokianga Harbour. Morphological and molecular data identified diverse cyanobacterial species (15 Oscillatoriales and five Nostocales), including close relatives of toxin producers. Genes associated with toxin production were not detected in any strains and their cellular extracts were not toxic to Artemia salina larvae. An in vitro feeding trial of Pacific oysters with a microcystin-producing Microcystis aeruginosa strain (CAWBG16) was undertaken. No microcystins were detected in the shellfish using liquid chromatography-mass spectrometry.