BACKGROUND Water hyacinth (Eichhornia crassipes) is a fast growing water weed that threatens the aquatic ecosystem and human activities, hence control of the plant is essential. One such control approach is to harvest and utilize hyacinth as a substrate for anaerobic digestion (AD). Various factors influence AD performance, including substrate pre-treatment and microbial community composition, amongst others. This study was aimed at establishing the link between method of substrate pre-treatment, microbial diversity, inoculum addition and biogas yield during AD of hyacinth. RESULTS The addition of an inoculum resulted in microbial community stability and early biomethane production of up to 0.4 L irrespective of pre-treatment method. However, cultures that lacked inoculum showed distinct microbial community structure variation in response to pre-treatment method, and minimal early biomethane production (up to 0.1 L). Biogas produced by cultures lacking inoculum was initially mostly composed of carbon dioxide (up to 100% of total biogas), but as digestion proceeded, an increase in biomethane production was observed (up to 60% of total biogas), which correlated with the shift in microbial community structure and increased microbial diversity. This indicates the presence of biogas-producing microorganisms associated with the collected hyacinth. Canonical correspondence analysis proved that dynamic changes in microbial community structure and biogas yield were strongly correlative. CONCLUSION This study proves that hyacinth pre-treatment influences microbial community structure and concomitant biogas yield in the absence of an inoculum. The addition of an inoculum aids in stability of microbial community structure and biogas yield irrespective of method of hyacinth pre-treatment. (c) 2019 Society of Chemical Industry