Method of mixed culture,earlier autotrophic condition and later heterotrophic condition, was used to enrich heterotrophic nitrifying bacteria and aerobic denitrifying bacteria from marine aquaculture wastewater. Heterotrophic nitrifying bacteria and aerobic denitrifying bacteria were isolated and purified by the heterotrophic culture medium. Using the special PCR primers, the bacteria were rapidly screened by amplifying Ammonia monooxygenase encoding gene (amoA) and a subunit of periplasmic nitrate reductase (NAR) encoding gene (napA). Those bacteria were identified by the denitrifying test. 22 heterotrophic bacteria strains were isolated, 11 strains had the amoA gene, 7 strains had both of the two genes, and there were 9 strains which had nitrifying ability.