The quaternary structure of the membrane-bound mannitol permease (EIIMtl) of the bacterial phosphotransferase system in Escherichia coli has been investigated in the membrane by using the radiation inactivation method. The experiments reveal two distinct but interconvertible forms of the permease. The first state is a dimer, and the second state consists of a less active higher molecular weight complex involving the dimer. The equilibrium between these two forms in the membrane can be shifted by changing the pH. At pH 8.1 the dimer is the dominant form. Decreasing the pH results in increased binding of a regulatory protein to the dimer, thus increasing the amount of the higher molecular weight form involving the dimer. Cross-linking EIIMtl in situ, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting, resulted in the formation of two cross-linked forms. One is the dimer, and the other has a higher molecular weight. Two-dimensional electrophoresis using a reversible cross-linker revealed no other protein except EIIMtl in these complexes.