Syntrophic relationships between fatty acid degrading bacteria and hydrogenotrophic methanogens are important for a well-functioning anaerobic degradation process during biogas production from organic waste material. This is particularly important in biogas processes fed protein-rich material as their degradation gives rise to high levels of ammonia, which inhibits many microorganisms. A common problem arising in the high-ammonia biogas process is the accumulation of volatile fatty acids, such as acetate, propionate or butyrate, which negatively affects the methane production. The aim of this study was to isolate and identify the syntrophic butyrate-oxidizing bacteria present in the enriched syntrophic communities originating from thermophilic continuously fed laboratory-scale reactors. Butyrate was added to batch assays containing the enrichment cultures. Sequencing of a 464 bp region within the 16S rRNA gene was conducted to study the change in microbial community structure over time during the butyrate degradation. The enrichment culture was also used as an inoculum source during the isolation attempts using agar cultivation, colony transfer and 16S rRNA gene sequencing of the obtained isolates. From the Illumina sequencing data, it could be concluded that the novel species of interest belonged to the genus Syntrophothermus. Two species were isolated, however neither appeared to be the butyrate-degrading bacterium. One of the species was Defluviitoga tunisiensis and the other was a novel species related to the mesophilic bacterium Schnuerera ultunensis.