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Feral goats are able to survive in many semi-arid areas of Australia. Under drought conditions, the only form of available feed is often mulga, which has a very high content of condensed tannins (5-24% dry weight). While feral goats apparently thrive on this diet, sheep do very poorly and lose liveweight rapidly. It has been shown that the transfer of rumen contents from feral goats to sheep can significantly improve mulga digestion, suggesting that the ruminal microflora of feral goats may contain tannin tolerant or degrading bacteria. To identify likely communities or associations of bacteria that may undertake this task, a comparative study of the bacterial ecology of the rumens of feral goats fed mulga and sheep fed either mulga or grass was undertaken. This study used the culture independent techniques of generation of 16S rDNA clone libraries and fluorescence in situ hybridisation (FISH) probing. From the clone libraries, bacteria were mainly (>90%) within the divisions Cytophaga-Flexibacter-Bacteroides (CFB) and low mol% G+C Gram positive bacteria (LGCGPB). In animals fed mulga, the CFB predominated (goat - 82% CFB and 11% LGCGPB; sheep - 78% CFB and 21% LGCGPB) whereas in sheep fed grass, the LGCGPB predominated (25% CFB vs 74% LGCGPB). In all clone libraries, few bacterial species were closely related to previously cultured bacteria, making it difficult to assign phenotypic traits. FISH probing of mulga fed -rumen (feral goats and sheep) or -fermentor samples demonstrated a predominance of CFB and gamma proteobacteria. This first molecular ecological study of tannin associated microbial communities suggested that bacteria from these two groups may be either more tolerant to tannins or able to degrade tannins. Further work will be required to elucidate the important members of these groups and to obtain them in culture.