F2 is one of two compound bioflocculant producing strains with good genetic stability and high flocculating activity. The core sequence of exoL was amplified from the F2 genome by the method of polymerase chain reaction, identifying that the effective polysaccharide component of bioflocculant produced by F2 was succinoglycan. The changes of protein complexes of F2 grown in minimal media versus bioflocculant media were researched by SDS-PAGE, indicating that in bioflocculant media compared with minimal media, the relative content of two protein complexes were obviously increased and the relative content of one protein complexes was obviously decreased in gels. It was three differentially expressed protein complexes that can probably induce the production of large amount of the effective polysaccharide component of bioflocculant produced by F2. The research can provide a step to reveal the molecular flocculating mechanisms of compound bioflocculant producing strains.