In recent years, several novel cation-independent bioflocculants have been reported, which can avoid the secondary contamination caused by addition of cations. However, compared with cation-dependent bioflocculants, the flocculating mechanism of cation-independent bioflocculants is largely unknown. In this study, a cation-independent bioflocculant MBF-W6 produced by Chryseobacterium daeguense W6 was used as a model to investigate the flocculating mechanism. The results showed that the major flocculating component of MBF-W6 is a complex of proteins and polysaccharides. The zeta potential results indicated that kaolin clay particles were not precipitated due to charge neutralization and the bridging mediated by cations did not play a major role in the flocculating process. These results are consistent with the fact that MBF-W6 is a cation-independent bioflocculant. Further scanning electron microscopic observation showed that MBF-W6 induced flocs formed tight packed structure, suggesting that the kaolin clay particles maybe directly attached and bridged by bioflocculant MBF-W6. In addition, we also found out that Fe 3+ ions inhibit the flocculating activity of MBF-W6 by affecting –COO - and –NH groups. Therefore this study can improve our understanding on flocculating mechanism of cation-independent bioflocculants.