The appropriate treatment of cyanide waste water is becoming an emerging issue because of the toxic residue and large quantity produced from gold processing plants. In the present article, we designed and operated a continuous biological cyanide treatment system using domestic sewage sludge and various microorganisms including a cyanide-producing and degrading bacterium, Chromobacterium violaceum. The synthetic wastewater containing 50 mg/L of cyanide was pumped continuously into the reactor at a flow rate of 500 mL/d for 21 days. When 50 mg/L of cyanide was fed, the cyanide concentration in the effluent of the reactor inoculated with activated sludge (S-50) decreased by 7.5 mg/L in the effluent. The other reactors did not show significant cyanide degradation and the reactor inoculated with C. violaceum showed increased cyanide concentration in the effluent. The microbial community in the reactors was analyzed by 16S rRNA-gene based pyrosequencing technique to investigate microbial response to cyanide addition and operation time. The microbial community analysis shows that the phylum Proteobacteria was detected in the reactors showing significant cyanide degradation (S-50), while Firmicutes and Bacteroidetes was dominant in the other reactors with very low cyanide degradation. Proteobacteria could not compete when the other phyla Firmicutes or Bacteroidetes were inoculated. This study shows the feasibility of the biological cyanide treatment system for gold processing plants and contributes new fundamental knowledge about the microbial community in the biological cyanide treatment system.