The fate of antibiotic resistance genes in anaerobic digestion systems and composting systems is presented from a research review and on-farm study. Generally, higher temperature systems (thermophilic rather than mesophilic) are more capable of reducing AR genes, however other variables play a role and more research is needed. An example of the impact of solid-liquid separation of dairy manure followed by in-vessel rotary drum composting of the separated solids is described from an on-farm study that found significant reduction (greater than 60%) of each of the AR gene copies after the compost treatment.