Lysogeny has been reported for a few freshwater cyanobacteria cultures, but it is unknown how prevalent it is in freshwater cyanobacteria in situ. Here we tested for lysogeny in (a) cultures of eight Australian species of subtropical freshwater cyanobacteria; (b) seven strains of one species: Cylindrospermopsis raciborskii; and (c) six cyanobacterial blooms in drinking water reservoirs in South East Queensland, Australia. Lysogenic infection in the cyanobacteria was induced through mitomycin C addition. By measuring the decline in host cell numbers and the concomitant increase in cyanophages over the course of the experiment, we observed lysogenic infection in five of the eight species of cyanobacteria (i.e. Nodularia spumigena, Anabaena circinalis, Anabaenopsis arnoldii, Aphanizomenon ovalisporum, Microcystis botrys, Microcystis aeruginosa, C. raciborskii and Anabaena spp., and in four of the seven strains of C. raciborskii) but only in two of the six natural cyanobacteria blooms. Lysogeny dominated laboratory culture strains whereas in natural blooms of cyanobacteria few species were lysogenic (i.e. not mitomycin C inducible). Thus, lysogenic laboratory cultures may not necessarily reflect the genetics nor the physiology of a natural cyanobacterial population, and more information on both forms is needed to understand better how cyanobacteria behave and exist in their natural habitat.