Carbonic anhydrase catalyses the interconversion of carbon dioxide and water to bicarbonate and protons. It was unknown if the industrial-relevant acetogen Clostridium autoethanogenum possesses these enzymes. We identified two putative carbonic anhydrase genes in its genome, one of the beta class and one of the gamma class. Carbonic anhydrase activity was found for the purified beta class enzyme, but not the gamma class candidate. Functional complementation of an Escherichia coli carbonic anhydrase knock-out mutant showed that the beta class carbonic anhydrase could complement this activity, but not the gamma class candidate gene. Phylogenetic analysis showed that the beta class carbonic anhydrase of Clostridium autoethanogenum represents a novel sub-class of beta class carbonic anhydrases that form the F-clade. The members of this clade have the shortest primary structure of any known carbonic anhydrase.