The biogas production and the composition of the microbial community in a pilot biogas plant fed exclusively with the above ground biomass (AGB) of Jerusalem Artichoke (JA) were assessed. Biochemical methane potential (BMP) tests, carried out with fresh, air-dried and ensiled above ground biomass of JA, showed that air-dried biomass of JA yielded the highest biogas production whereas the ensiled biomass showed the lowest one. Similar results were obtained from the pilot plant as best results in terms of biogas production and methane volume fraction were associated with air-dried JA. The structure and dynamics of the microbial community involved in biogas production were studied using denaturing gradient gel electrophoresis (DGGE) method. The genus Methanoculleus predominated among methanogenic Archaea, indicating that biomethane was mainly produced through the hydrogenotrophic pathway. In general, there are no significant differences in microbial community structure when the reactor is fed either with air-dried or ensiled JA.