The combination of environmental concerns and the growing demand for energy make the development of biofuels, an attractive alternative to fossil fuels, a goal for many researchers. The direct photosynthetic production of hydrocarbons, which are the major components of fossil fuels, is considered to be a promising and innovative strategy for the development of biofuels with advanced fuel properties and solar-driven energy input. Cyanobacteria have existed continuously since the early evolution of the biosphere and the biosynthetic pathways of hydrocarbons in these prokaryotes have been genetically and biochemically identified. In this study, the hydrocarbon compositions of 19 freshwater cyanobacterial species distributed among 13 genera were analyzed. Based on their hydrocarbon profiles, these cyanobacterial species were classified into 5 major subgroups. Combined with the previously reported hydrocarbon compositions in different cyanobacterial species, we found that branched-chain alkanes were limited predominantly in filamentous species but rarely in unicellular species. Phylogenetic analysis using traditional small-subunit ribosomal RNA (16S rDNA) of these strains presented clustering similar to their hydrocarbon production profiles. Acyl-acyl carrier protein reductase (AAR) and aldehyde deformylating oxygenase (ADO) are two key enzymes involved in the biosynthesis of hydrocarbons in cyanobacteria. A comparison of phylogenies revealed that the topology of 16S rDNA showed a general congruence with that of AAR but not with that of ADO. The results not only provide an evolutionary perspective with which to study the physiological function of cellular hydrocarbons but also display the engineering capacity to molecularly design diversified hydrocarbon fuel products in cyanobacteria. (C) 2013 Elsevier Ltd. All rights reserved.