Rhodococcus opacus R7 is a naphthalene-degrading microorganism which is also able to grow on o-xylene. This work describes the isolation and analysis of two new genomic regions in which genes involved in naphthalene (nar gene cluster) and salicylate (gen gene cluster) degradation are located. In the nar gene cluster we found: two genes encoding the large (narAa) and the small (narAb) components of the naphthalene dioxygenase, three genes (rub1, rub2, rub1bis) encoding three rubredoxins, an orf (orf7) associated to the complex encoding a protein of unknown function, two regulatory genes (narR1, narR2), a gene (narB) encoding the naphthalene dihydrodiol dehydrogenase and six orfs (orf1, orf2, orf3, orf4, orf5, orf6) encoding proteins of unknown function. In the gen gene cluster, we found the following genes: two genes encoding the salicylate CoA ligase and the salicylate CoA synthetase (genA and genB), respectively, a gene (genC) encoding a salicylate hydroxylase, a gene (genH) encoding a gentisate 1,2-dioxygenase, a gene (genI) encoding a 3-maleylpyruvate isomerase, and a gene (genL) encoding a protein of unknown function. The transcription of some genes of R. opacus R7 strain grown on different substrates was also investigated to evaluate the expression of the two gene clusters after cDNA preparations.