In agricultural biogas plants, anaerobic digestion decomposes organic matter into biogas and digestate. In addition to corn silage, the input component is livestock manure or slurry. The origin of the slurry affects to some extent the composition of the bacterial community in the digester. The liquid output (fugate) is usually applied to arable land as fertilizer. The aim of the experiment was to compare the diversity of bacterial communities in fugate originating from biogas plants processing cattle, swine and poultry manure as input raw material. The bacterial community was analysed based on 16S rRNA at the order level and the diversity of bacteria was compared by fragment analysis of ribosomal RNA. Significant differences in the composition of the bacterial community were found between the fugates, but in all cases the order Clostridiales significantly dominated.