Isotopic data indicate that coalbed methane (CBM) in many Australian reservoirs comprise secondary biogenic gas, however, little is known of the microbes active in these reservoirs. Therefore, for the first time in Australia, a preliminary culture-independent survey of the prokaryotic microbial composition of some of these reservoirs was undertaken to provide a basis for an understanding of the origin of the observed biogenic gas. Four water and three coal samples from the east coast of Australia were examined for their prokaryotic diversity by 16S rDNA analysis. DNA was extracted from the samples and amplified using bacterial- and archaeal-selective primers, and the resulting amplicons were cloned and sequenced. DNA amplicons derived from Gram-negative bacteria predominated; relatively few archaeal and Gram-positive bacterial sequences were amplified from the original samples. By-and-large coal samples yielded almost exclusively archaeal and α-proteobacterial amplicons, whereas the water samples contained amplicons derived from the remaining proteobacteria (β-ε) and bacteroidetes. Amplicons from three genera of archaea were observed, none of which were genuine methanogens, although the dominant genus, Archaeoglobus, is reported to have some weak methanogenic activity. Further integrated studies of microbiology, hydrochemistry, gas geochemistry and geology of CBM reservoirs are continuing in order to better understand the parameters for methane production in eastern Australian basins.