The aim of this study was to evaluate the contribution of dissolved organic carbon (DOC) and microbial community dynamics to membrane fouling development in membrane bioreactor (MBR). We operated laboratory-scale anoxic/oxic-MBRs under prolonged starvation conditions in different seasons and the dynamics and diversity of the microbial communities were investigated. Although fouled-MBRs showed DOC accumulation in the activated sludge (AS), the fouling-mitigated MBR suggested that dissolved oxygen was consumed and DOC of the sludge supernatant was degraded. 16S rRNA genes analysis of AS in the MBRs revealed that Chitinophagaceae and Candidatus Promineofilum specifically increased in the fouling-mitigated MBR, suggesting that they played important roles in membrane fouling mitigation; high microbial diversity in the reactor also contributed to fouling mitigation. In the fouled reactor, enrichment of Xanthomonadaceae might be related to fouling causing substances formation leading to membrane fouling development; lower microbial diversity also contributed to fouling development in the fouled MBR.