The classification of bacteria may lead to the understanding of evolution of microorganisms. Until now, the coding structure of nucleotide sequences is assumed to have the different structure. That is, the classification information of biological organism can be mined via resolving the coding structure of nucleotide sequences. In this article, we proposed a systematic procedure based on the integrated clustering techniques to address such issue. Expect for the clustering techniques, the core function of the proposed approach also include the necessary data transformation and dimension reduction. A significant contribution, which is the clustering of biological organisms, can be made by using the systematic procedure based on integrated clustering technique. Restated, the biologists can apply the proposed systematic procedure to get the initial sense for the classification of biological organisms, and it will shorten the early analytic time. In this study, an illustrative example will be employed to demonstrate the feasibility and rationality of the proposed procedure in this article.