Late-summer blooms of the Nostocalean cyanobacteria Nodularia spumigena, Aphanizomenon flos-aquae and Anabaena spp., occur annually over vast areas of the Baltic Sea. Apart from the planktonic bloom period, the annual cycle of these cyanobacteria is poorly known. With a combination of pelagial monitoring, sedimentation traps and germination experiments, we studied the annual cycle of formation, sedimentation and germination of cyanobacterial akinetes (resting stages) in the northern Baltic Sea during 2005–2006. Akinetes were only rarely encountered in the fall plankton, but they were abundant in the near-bottom sedimentation trap from the middle of July to August. All three taxa formed akinetes, but the numbers of A. flos-aquae akinetes were generally low. Of the three taxa, only Anabaena spp. were regularly found to germinate from the sediment samples. Estimates of Anabaena viable seed bank size ranged from 205 to 1913akinetesg−1(ww) of sediment. Aphanizomenon flos-aquae never germinated, and N. spumigena did so only occasionally. It is concluded that the three co-occurring taxa probably have different life cycle strategies, A. flos-aquae being holoplanktonic and Anabaena spp. planktonic during summer, but overwintering as akinetes in the bottom. Summer populations of N. spumigena may originate from both sedimented akinetes and trichomes that overwinter in the water column.