The impact of long-term organic and inorganic fertilizer amendments on microbial community structure was assessed using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis of selected microbial groups and PhosphoLipid Fatty Acid (PLFA) profiling. Over three time-points (May, September 2004 and January 2005) soil samples were taken from 13 plots at the Palace Leas experimental hay meadow site in Northumberland, UK. These plots were established in 1897 and have received either no amendment; Farm Yard Manure (FYM) with or without inorganic N, P and K; or factorial combinations of inorganic N, P and K. To generate group specific T-RFLP profiles, primers specific to the SSU rRNA genes of nematodes, Arbuscular Mycorrhizal (AM) fungi, actinobacteria and Ammonia-Oxidizing Bacteria (AOB) were used. Preliminary multivariate analysis of the T-RFLP profiles revealed large temporal shifts in the microbial community structure throughout the year which masked any overall effect of treatment. However, within individual time points management regime did have an impact on the communities, but these effects were not consistent either between the microbial groups or across time points. The AM fungal communities differed between the FYM or inorganic-only fertilized plots at all three time points whereas the nematode populations differed at only two time points. The actinobacteria T-RFLP profiles revealed no differences between soils receiving FYM or inorganic-only amendments except where the inorganic fertilizer input (as NH₂SO₄) had resulted in a change in soil pH. The PLFA profiles were extremely stable throughout the year and revealed no direct influence of FYM or inorganic-only fertilizer treatments on the microbial community structure. Instead differences in PLFA profiles appeared to be indirectly linked to management regime with the communities falling into three groups correlated with soil pH. These results highlight the importance of considering individual components of the microbial community and reveal how long-term organic and inorganic fertilizer amendments can have large, direct and indirect, impacts on different microbial populations.