Various salinities affected the PAH-biodegrading community structure. Various salinities affected the growth of strains with different salt tolerance. The two genes belonged to a new divergent cluster of the known -like genes. The two main genes had correlations with the phenanthrene degradation. The aim of this study is to analyze the effect of salinity on polycyclic aromatic hydrocarbons (PAHs) biodegradation, community structure and naphthalene dioxygenase gene ( ) diversity of a halophilic bacterial consortium with the denaturing gradient gel electrophoresis (DGGE) approach. The consortium was developed from oil-contaminated saline soil after enrichment for six times, using phenanthrene as the substrate. The prominent species in the bacterial consortium at all salinities were identified as halophilic bacteria , , , , and uncultured bacteria. The predominant microbes gradually changed associating with the saline concentration fluctuations ranging from 0.1% to 25% (w/v). Two alpha subunits were dominant at salinities ranging from 0.1% to 20%, while not been clearly detected at 25% salinity. Consistently, the biodegradation occurred at salinities ranging from 0.1% to 20%, while no at 25% salinity, suggesting the two genes played an important role in the degradation. The phylogenetic analysis revealed that both of the two alpha subunits were related to the classic -like gene from AN10 and PaK1, while one with identity of about 82% and the other one with identity of 90% at amino acid sequence level. We concluded that salinity greatly affected halophilic bacterial community structure and also the functional genes which were more related to biodegradation.