Nowadays, the increase of the unconventional oil deposit exploitation and the amount of oil sands process-affected waters (OSPW) in tailing ponds emerges the importance of developing bio-monitoring strategies for the restoration of these habitats. The major constituents of such deposits are naphthenic acids (NAs), emerging contaminant mixtures with toxic and recalcitrant properties. With the aim of developing bio-monitoring strategies based on culture-independent approach, we identified genes coding for enzymes involved in NA degradation from Rhodococcus opacus R7 genome, after the evaluation of its ability to mineralize model NAs. R. opacus R7 whole-genome analysis unveiled the presence of pobA and chcpca gene clusters putatively involved in NAs degradation. Gene expression analysis demonstrated the specific induction of R7 aliA1 gene, encoding for a long-chain-fatty-acid-CoA ligase, in the presence of cyclohexanecarboxylic acid (CHCA) and hexanoic acid (HA), selected as representative compounds for alicyclic and linear NAs, respectively. Therefore, aliA1 gene was selected as a molecular marker to monitor the biodegradative potential of slurry-phase sand microcosms in different conditions: spiked with CHCA, in the presence of R. opacus R7, the autochthonous microbial community, and combining these factors. Results revealed that the aliA1-targeting culture-independent approach could be a useful method for bio-monitoring of NA degradation in a model laboratory system.