Comprehensive lipid biomarker profiles were determined for extant intertidal columnar stromatolites and non-lithified smooth and pustular microbial mats from Hamelin Pool, Shark Bay, Western Australia. Hydrocarbons, alkyl (wax) esters, sterols, fatty acids, triterpenoids and ether-linked hydrocarbons were analysed using gas chromatography-mass spectrometry (GC-MS) and triterpenoids were analysed using high temperature GC-MS. Cyanobacterial markers were abundant in each sample and lipids diagnostic of heterotrophic bacteria, sulfate-reducing bacteria, anoxygenic phototropic bacteria and archaea were also detected. Limited input from higher plants and diatoms was observed. For the first time, 2-methylhopanoids were detected in Hamelin Pool microbial communities. The overall lipid profiles of the three sediment types were similar, suggesting that extant non-lithified microbial mats and stromatolites can comprise similar microbial communities.