One hundred and four taxa of planktonic cyanobacteria (blue‐green algae) have been recorded from New Zealand lakes: 32 belong to the Chroococcales, 72 to the Nostocales. None of the taxa is endemic to New Zealand; most (if not all) are cosmopolitan. On average, more taxa have been reported from North Island (7.8 ± 6.7,N= 69) than South Island lakes (3.3 ± 3.9,N= 59). This difference is attributable, in part, to the large proportion of glacial lakes in the South Island, which are commonly poor in plant nutrients and possess sparse phytoplankton populations. Many of the taxa show a strong preference for eutrophic conditions. Notable exceptions areAnabaena affinisandGomphosphaeria lacustris, which occur in a large proportion of mesotrophic (48%) and oligotrophic lakes (43%), respectively. Taxa which are often abundant and frequently responsible for conspicuous water‐blooms areMicrocystis aeruginosa, Anabaena circinalis, A. flos‐aquaeandA. spiroides. The limited population data available indicate a high level of interannual variability in the timing, magnitude, and duration of cyanobacterial blooms in New Zealand lakes.