The aim of this study is to identify three kinds of black-pigmented periodontal pathogens P. gingivalis Pg, P. intermedia Pi, P. nigrescens Pn by 16S rDNA and microarray.A pair of universal primers which can amplify a section of conservative domain of bacterial 16S rDNA based on the sequences of 16S rDNA in Genebank were designed. Then the specific oligonucleotide probes for Pg Pi Pn based on the sequences of the conservative domain were constructed. Standard bacterial genomic DNAs were amplified using the designed universal primers by PCR, and labeled by digoxigenin at the same time, the products of PCR were hybridized with the microarray in which the specific probes were added. The results of hybridization were analysed.The results of hybridization showed that the specific probes of Pg Pi Pn on microarray reacted only with corresponding PCR products of Pg Pi Pn, not reacted with others.The method of 16S rDNA and membrane microarray could be useful to identify Pg Pi Pn, and had high specificity. It will be developed into a kind of clinical bacterial detective system.