To investigate the effect of long term application of organic matter in upland soils, plots for treatments of NPK, NPK+pig manure compost, rape seed cake, rice straw compost, and green manure were set up. Populations of Bacillus and Gram negative bacteria were high in the plot treated with green manure application, but microbial biomass was increased with chemical fertilizer or pig manure compost in upland soils. Activities of phosphomonoesterase and dehydrogenase were high with organic matter application comparing to control. Cluster patterns analysed using phospholipid fatty acid of plots treated with rice straw and or pig manure compost were clearly different comparing with other treatments. Dominant bacteria in upland soils were Bacillus flexus, B. subtilis and B. megaterium. And the strains isolated from upland soils had amylase, protease and lipase activities.