Three agricultural by products (CHO:wheat straw, apple pulp and sugar beet pulp) as substrate plus 2 levels of freeze-dried cow’s feces (C0-i: 5 and 10 %) as co-inoculum were assigned in quadruplicate during 56 days of in vitro fermentation. Bottles were sampled at days (D) 0, 25 and 56 to determine the evolution of total bacteria, total and hydrogenotrophic methanogens archaea. DGGE was used to study archaea biodiversity in the slurry incubations. CHO addition did not alter bacteria titres but co-i interacts with D (P<0.001), in 5% total bacteria decreased significantly (d0 to d25) but remained steady until d56 (P>0.05) whereas in 10% titres decrease constantly (P<0.05). Incubation time also reduced the titres of archaea (P<0.01). However, hydrogenotrophic population maintained titres along incubation period and increased with Co-i (P<0.05). Most of the archaeal DGGE bands were observed in all samples, indicating a common bacterial population origin and their structure showed that incubation time and Co-i can modify the clustering pattern.