Early warning indicators (EWIs) and microbial community dynamics during thermophilic dark fermentation-based hydrogen production (TFHP) from food wastes were investigated during stable and fluctuating operations in continuous systems. Difference and redundancy analyses revealed the linkage between dominant genera, metabolites and process parameters and characterized the EWIs and mechanism of instability of the TFHP. Besides biogas production rate (GPR), hydrogen proportion and volatile fatty acids (VFAs) concentrations, the potential warning function of the microbial community were observed. Thermoanaerobacterium was the dominant genus which decreased during the unstable stages. Bacillus is another EWI in unstable stages when the value of pH is lower. Lactobacillus and Weissella appeared as OLR increased to 9 g VS L-1 d(-1) in the OLR-9 unstable stage. This study demonstrates the key EWIs for monitoring and controlling continuous hydrogen production and its stability. (C) 2019 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.