Polycyclic aromatic hydrocarbons such as naphthalene are recalcitrant environmental pollutants that are only slowly metabolized by bacteria under anoxic conditions. Based on metabolite analyses of culture supernatants, carboxylation or methylation of naphthalene have been proposed as initial enzymatic activation reactions in the pathway. However, the extremely slow growth of anaerobic naphthalene degraders with doubling times of weeks and the little biomass obtained from such cultures hindered the biochemical elucidation of the initial activation reaction, so far. Here, we provide biochemical evidence that anaerobic naphthalene degradation is initiated via carboxylation. Crude cell extracts of the sulfate-reducing enrichment culture N47 converted naphthalene and 13C-labelled bicarbonate to 2-[carboxyl-13C]naphthoic acid at a rate of 0.12 nmol min−1 mg protein−1. The enzyme, namely naphthalene carboxylase, catalysed a much faster exchange of 13C-labelled bicarbonate with the carboxyl group of 2-[carboxyl-12C]naphthoic acid at a rate of 3.2 nmol min−1 mg protein−1, indicating that the rate limiting step of the carboxylation reaction is the activation of the naphthalene molecule rather than the carboxylation itself. Neither the carboxylation nor the exchange reaction activities necessitate the presence of ATP or divalent metal ions and they were not inhibited by avidin or EDTA. The new carboxylation reaction is unprecedented in biochemistry and opens the door to understand the anaerobic degradation of polycyclic aromatic hydrocarbons which are among the most hazardous environmental contaminants.