A technology of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to profile the structure and dynamic changes of microbial communities in a bioreactor for treating hydrocarbon-sulfide-containing (HSC) wastewater. The results showed that the heterotrophic genus of Acinetobacter and the autotrophic genera of Thiobacillus and Thiomonas could survive well in all of three operating conditions. Some special genera were also observed with changes of micro-ecoenvironment in the reactor, such as the halophilic genus of Nesterenkonia. Further, a new genus was found in the reactor, which was likely to have the ability to degrade sulfide and hydrocarbon at the same time. All of these detected and the new found genera have widely applicable potential in the treatment of HSC wastewater.