Surfactants can affect the biodegradation process and the fate of hydrophobic organic compounds (HOCs) in the environment. Previous studies have shown that surfactants can enhance the biodegradation of HOCs by increasing cell surface hydrophobicity (CSH) and membrane fluidity. In this study, we took this work one step further by investigating the expression levels of three genes of Arthrobacter sp. SA02 in the biodegradation of phenanthrene as a typical HOC at different concentrations of sodium dodecyl benzenesulfonate (SDBS), which is a widely used surfactant. The Δ9 fatty acid desaturase gene codes for Δ9 fatty acid desaturase, which can convert saturated fatty acid to its unsaturated form. The ring-hydroxylating dioxygenase (RHDase) and the 1-hydroxyl-2-naphthoate dioxygenase (1H2Nase) genes code for the RHDase and 1H2Nase enzymes, respectively, which play a key role in decomposing doubly hydroxylated aromatic compounds. The results show that these three genes were upregulated in the presence of SDBS. On the basis of the genetic and physiological changes, we proposed a pathway that links the gene expression with the physiological phenomena, including CSH, membrane fluidity, and intracellular degradation. This study advances our understanding of the surfactant-enhanced biodegradation of HOCs at the gene level, and the proposed pathway should be further validated in the future.