The Taiwan Chelungpu Drilling Project (TCDP) has provided an unprecedented opportunity to reveal a terrestrial subsurface microbial ecosystem that has possibly experienced continuous disturbance by the arc-continental collision since 5 Ma. The drilling penetrated Pliocene-Pleistocene sedimentary rocks to a depth of 2000 meters below the land surface (mbls) and encountered two major fault zones. Sixteen samples retrieved from the drilled cores at depths between 464 to 1451 mbls were examined to characterize microbial community structures through cultivation-based approaches. Cultivation experiments were performed with various media at temperatures ranging from 30 to 50°C. The results indicate that fermenters and heterotrophic sulfate reducers, using complex organic carbon, were ubiquitously present in most samples. Acetate-utilizing and H2-utilizing sulfate reducers were restricted to shallower intervals along the depth profile. Iron reducers and methanogens were only cultivated in a few shallow samples. Twelve pure strains including 8 fermenters, 3 iron reducers and 1 sulfate reducer originally enriched at 30 or 40°C were isolated and identified with 16S rDNA sequence analyses. They were phylogenetically affiliated with Firmicutes, Bactetiodes, Actinobacteria, and Proteobacteria in various degrees of similarity. The presence of metabolism was not correlated with lithology, depth, temperature and the appearance of fracture throughout the core. The ubiquitous appearance of fermentation and organotrophic sulfate reduction suggests that organic carbon sources were readily accessible in this deep terrestrial subsurface environment. These results infer that the foreland sedimentary strata disturbed by tectonic activities over a geological time scale might support a heterotrophy-dominated deep terrestrial subsurface microbial ecosystem.