We investigated the potential for the ultradeep Au mines of South Africa to provide unique "windows" into the deep, continental biosphere through which a detailed analysis of microbial communities as a function of various environmental parameters could be performed. The depths and pressures of these mines approach those at ocean ridges and the temperatures of the mined formations lie within the zone for microbial thermophilicity (45-70oC). The microbial communities encountered in these mines are composed of a mixture of contaminating (allochthonous) and indigenous (autochthonous) microorganisms. To distinguish autochthonous from allochthonous microorganisms we developed sample collection and processing techniques that quantified and minimized the allochthonous bacterial contaminants in the mine samples. This permits evaluation of the relationship between the indigenous microbial communities and large-scale hydrogeochemical facies as well as small scale geochemical heterogeneity.