Abstract: Seasonal and depth wise variation in bacterial and fungal populations was studied in three arecanut-based traditional agroforestry systems practiced by two ethnic communities viz., the Kalitas and Nyishis. Arecanut palm was abundantly found in Harmutty and this site also recorded greater species diversity. Soil was sandy loam in all sites. Soil organic C, total N and available P decreased with increasing soil depth. Bacterial population was highest during spring and that of fungi during autumn. Nonetheless, the highest microbial counts were recorded in the topsoil (0-10 cm) layer except during the rainy season when the population was greater in the subsurface (10-20 cm) layer. Altogether, 29 soil micro-fungal forms were recorded from three sites. Aspergillus and Penicillium were the abundant genera in the sites. Soil organic C and total N concentration had correlation with the microbial colony forming units. It was noticed that plant residues, added organic matter, vegetation, plant species composition and soil mineral nutrients altered the microbial population as well as their species composition under traditional agroforestry system.