In this paper, four compound bacteria for degrading phenanthrene or naphthalene were acclimated from the polluted farmland soil nearby a coke-plant as well as the activated sludge from a waste water plant, in which the compound bacteria from the activated sludge gave a degradation efficiency of 85.90% and 79.45% in 96 hours to phenanthrene and naphthalene, respectively and those from the polluted farmland soil with a degradation efficiency of 52.63% and 52.15% to phenanthrene and naphthalene, respectively. In order to compare the community structure and diversity in these compound bacteria, the V3-V4 regions in bacterial 16S rDNA were sequenced using the Illumina Miseq platform, by which a total of 420,771 filtered sequences of 16S rDNA were obtained from 4 compound bacteria and subsequently clustered into 10,696 OTUs（operational taxonomic units）, with most of OTUs unique for each community. The order of species richness for different community was the soil phenanthrene-degrading compound bacterium＞the sludge naphthalene-degrading compound bacterium＞the soil naphthalene-degrading compound bacterium＞the sludge phenanthrene-degrading compound bacterium, while that of species diversity was the soil phenanthrene-degrading compound bacterium＞the sludge naphthalene-degrading compound bacterium＞the sludge phenanthrene-degrading compound bacterium ＞ the soil naphthalene-degrading compound bacterium. On the genus-level classification, the dominant bacteria in the soil phenanthrene-degrading compound bacterium included Enterobacter（38.21%）, Comamonas（32.78%） and Acinetobacter（20.49%）, and those in the soil naphthalenedegrading compound bacterium were comprised of Enterobacter（85.16%） and Acinetobacter（9.67%）. On the other hand, the dominant bacteria in the sludge phenanthrene-degrading compound bacterium came from Stenotrophomonas（90.58%）, and those for the sludge naphthalene-degrading compound bacterium consisted of Acinetobacter（52.74%） and Enterobacter（40.11%）. This study developed the phenanthrene-or naphthalene-degrading compound bacteria with high species richness and diversity, which can be used to remediate the polluted soil or water by polycyclic aromatic hydrocarbons.