The diversity of methanogens in the rumen of sheep fed three different diets was examined using denaturing gradient gel electrophoresis (DGGE). In addition, half of the sheep had pot scrubbers added to their rumen to increase flow rate. The methanogens were separated by a series of washing steps into three populations: free-living, ecto-symbiotic and endo-symbiotic. Preliminary DGGE banding patterns demonstrated considerable differences between populations, treatment groups, and within groups. This suggests that the diversity of methanogens is influenced by diet, flow rates of digesta and the niche they occupy in relation to the protozoa.