We collected soil samples from two representative sites at Aatmile of Khagarachari hill district in Chittagong Hill Tracts. One of the sites was under shifting cultivation and the other an adjacent 13-year old teak plantation. Both sites were in the same physiographic condition and same aspect with parable soil type, which enabled us to measure the effects of shifting cultivation on soil micro-flora. We studied soil physico-chemical properties and the biochemical and biological properties of soil microbes. Moisture and organic matter content as well as fungi and bacterial populations, both in surface and subsurface soils, were significantly(p ≤0.001) lower in shifting cultivated soils compared to soils not under shifting cultivation, i.e. the teak plantation site. The most abundant bacteria in surface(0-10 cm) and sub-surface(10-20 cm) soils under shifting cultivation were Pseudomonas diminuta and Shigella, respectively, while in corresponding soil layers of teak plantation, predominant microbes were Bacillus firmus(0-10 cm) and Xanthomonas(10-20 cm). The microbial population differences cannot be explained by soil texture differences because of the textural similarity in soils from the two sites but could be related to the significantly lower moisture and organic matter contents in soils under shifting cultivation. We collected soil samples from two representative sites at Aatmile of Khagarachari hill district in Chittagong Hill Tracts. One of the sites was under shifting cultivation and the other an adjacent 13-year old teak plantation. Both sites were in the same physiographic condition and same aspect with parable soil type, which enabled us to measure the effects of shifting cultivation on soil micro-flora. We studied soil physico-chemical properties and the biochemical and biological properties of soil microbes. Moisture and organic matter content as well as fungi and bacterial populations , both in surface and subsurface soils, were significantly (p ≤ 0.001) lower in shifting cultivated soils compared to soils not under shifting cultivation, ie the teak plantation site. The most abundant bacteria in surfaces (0-10 cm) and sub-surfaces (10-20 cm) soils under shifting cultivation were Pseudomonas diminuta and Shigella, respectively, while in corresponding soil layers of teak plantation, predomin The microbes were Bacillus firmus (0-10 cm) and Xanthomonas (10-20 cm). The microbial population differences can not be explained by soil texture differences because of the textural similarity in soils from the two sites but could be related to the significantly lower moisture and organic matter contents in soils under shifting cultivation.