Succinate:quinone reductase catalyzes electron transfer from succinate to quinone in aerobic respiration. Carboxin is a specific inhibitor of this enzyme from several different organisms. We have isolated mutant strains of the bacterium Paracoccus denitrificans that are resistant to carboxin due to mutations in the succinate:quinone reductase. The mutations identify two amino acid residues, His228 in SdhB and Asp89 in SdhD, that most likely constitute part of a carboxin-binding site. This site is in the same region of the enzyme as the proposed active site for ubiquinone reduction. From the combined mutant data and structural information derived from Escherichia coli and Wolinella succinogenes quinol:fumarate reductase, we suggest that carboxin acts by blocking binding of ubiquinone to the active site. The block would be either by direct exclusion of uhiquinone from the active site or by occlusion of a pore that leads to the active site.