A study was conducted at two pair sites of Chittagong Hill Tracts in Bangladesh to find out the effects of shifting cultivation on soil fungi and bacterial population. The first pair of sites with shifting cultivation and village common forest-managed by indigenous community was at Madhya Para in Rangamati district and the second pair of sites with the shifting cultivated land and village common forest at Ampu Para in Bandarban district of Chittagong Hill Tracts. At both the locations with two different land uses, soil textures in surface (0-10 cm) and subsurface (10-20 cm) soils varied from sandy loam to sandy clay loam. Soil pH and moisture content were lower in shifting cultivated land compared to village common forest. The results also showed that both fungal and bacterial population in surface and subsurface soils was significantly (p≤0.05) lower, in most cases, in shifting cultivated land compared to village common forest at both Madhya Para and Ampu Para. At Rangamati and Bandarban in shifting cultivated lands, Colletrotrichum and Fusarium fungi were absent and all the bacterial genus viz. Coccus,Bacillus and Streptococcus common in two different locations with different land uses. Common identified fungi at both the land uses and locations were Aspergillus, Rhizopus, Trichoderma and Penicillium.Further study can be done on the other soil biota to understand the extent of environmental deterioration due to shifting cultivation.