Cyanobacteria are ubiquitous, ecologically important and phylogenetically diverse components of the phytoplankton of marine and freshwater environments, as well as some extreme settings such as hot springs, and highly saline and ice covered lakes. They have also been shown to be amongst the most prolific sources of bacteriohopanepolyols (BHPs; pentacyclic triterpenoids produced by taxa within the bacterial domain and especially in the proteobacteria) and are considered to be the most environmentally significant source of C-2 methylated hopanoids. The compounds therefore have the potential for wide application in studies of the contemporary marine carbon cycle as well as providing a means of tracking cyanobacteria back through geological history where organic matter is well preserved. Here, we have used liquid chromatography ion-trap mass spectrometry to investigate the intact BHP distributions in cultured cyanobacteria (pure cultures and enrichment cultures) and in a variety of environmental settings. We present data on the detection and characterisation of BHP structures in 26 cultured cyanobacteria (ranging from marine and freshwater species to isolates from hydrothermal systems), 10 of which have not been tested for hopanoid production. Of the 58 strains of cyanobacteria studied to date, 49 have been shown to produce BHPs and 21 of them produce C-2 methylated BHPs. We show that, paradoxically, hopanoid production appears to be absent from the most prolific marine picocyanobacteria, although two important marine nitrogen fixing species, Trichodesmium and Crocosphaera, do produce BHPs. The diversity of BHP distributions in a range of environmental samples, including lake sediments, bacterial mats from lakes and hydrothermal springs, and samples from hot and cold deserts, including endoliths, hypoliths and small stromatolitic structures is also described.