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Four lab scale biogas reactors fed with a substrate composition of ensiled fish waste and manure fixed at 13 and 87 vol %, respectively, were operated with HRTs of 20, 25, 30 and 40 days. Biogas process performance and stability were evaluated with regard to CH4 yields, NH4+ accumulation and abundance of NH4+-tolerant microorganisms. Process performance in the reactors operated at different HRTs were compared to process performance in reactors operated with constant HRT, fed with increased ratios of fish waste. The process performance and microbial dynamics were stable in reactors operated at constant amount of fish waste in the feed and with different HRTs. In the reactors added elevated ratios of fish waste, the concentration of NH4+ and abundance of NH4+-tolerant acetate oxidizing bacteria increased. The biogas process failed in these reactors simultaneously with an observed shift in microbial composition. In particular, the bacterium Tepidanaerobacter Acetatoxydans seemed to affect the biogas process stability. The hydrogenotrophic Methanomicrobiales increased in abundance in response to higher fish waste loading and NH4+ concentrations. This study showed that at a loading of 13% fish waste, it is possible to decrease the HRT from 30 to 20 days without markedly inhibiting the process stability.