Few studies have examined the potential long-term effects of high concentrations of hexahydro-1,3,5-trinitro-1,3,5-triaxine (RDX) on bacterial communities in soil. In the present study, a sandy loam soil and a silt loam soil (high and low bioavailability, respectively) were artificially contaminated with RDX (0, 50, 500, 1,500, 5,000, 10,000, and 15,000 mg/kg soil). Bacterial communities from each treatment were monitored over 63 d to characterize the effects of RDX exposure on bacterial activity, biomass, functional diversity (Biolog microtiter plates), and structural diversity (denaturing gradient gel electrophoresis of 16S rDNA). Bacterial communities native to the high bioavailability soil were inherently different than bacterial communities native to the silt loam soil, not only in terms of bacterial activity and biomass, but also in terms of bacterial community functional and structural diversity. Soil RDX contamination was correlated with decreased bacterial biomass in the silt loam soil treatments and with decreased bacterial activity in the sandy loam soil treatments on day 7. Soil RDX contamination did not cause a significant shift in the functional diversity of the bacterial communities native to the silt loam soil, but was correlated with a shift in identities of substrates used by bacterial communities native to the sandy loam soil on day 7. Bacterial community structure was insensitive to the gradient of RDX concentrations at the beginning of the incubation. However, the identities of carbon substrates used by bacterial communities in both soil types were affected by long-term incubation with RDX.