Anaerobic digestion converting organic material into biogas is an attractive strategy for sustainable waste management and production of renewable energy. The goal of this study was to investigate community dynamics in two parallel CSTR-reactors co-digesting cow-manure and whey permeate a by-products from cheese production considered as a suitable substrate for biogas production. These two reactors differed in performance (accumulation of intermediate products and methane production) over time, giving us an opportunity to study the microbial dynamics of two initially identical anaerobic digestion processes apparently operating on boundary of tolerance.