Background Anaerobic digestion is a microbial driven process, which results in biogas production. Although important, the relative abundance of microbial communities can be affected by disturbances such as feeding rates. In this study, the effects of irregular organic loading rates on anaerobic digestion of water hyacinth (mono- and co-digestion) as well as on bacterial and archaeal communities were investigated. The process was conducted at different feeding stages during which the process stability, biogas production, composition and microbial community structure were monitored. Results Bacterial communities were more influenced by irregular organic loading rates in comparison with archaeal communities. Although microbial community shifts were observed in both mono- and co-digestion, the shift was more prevalent in co-digestion. Moreover, process stability was evidenced in some stages of mono-digestion, where the FOS/TAC ratio was within the optimal range. However, for co-digestion, the low FOS/TAC ratio showed process instability. Conclusion Overall, irregularity in organic loading rates affected the microbial community composition as well as their CH4 production. (c) 2018 Society of Chemical Industry