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Arbuscular mycorrhizal fungi (AMF) and dark septate endophyte (DSE) colonization were investigated in three different plantation sites (Umdihar,Umsaw and Mawlein) of Meghalaya,northeast India. Isolation and identification of the AMF spore were conducted to evaluate the AMF diversity and host preference in terms of AMF species distribution and abundance in the plantation sites. Results showed that AMF colonization was significantly higher than dark septate endophyte colonization (p>0.05). AMF and DSE colonization had a narrow range of colonization,varying from 50.91%-58.95% and 1.84%-4.11%,respectively. Spore density varied significantly in all the sites (p>0.05). Out of 29 species identified from 7 genera,the species from Glomus was found to be highly abundant. Sorenson coefficient (Cs) ranged from 0.35-7.0. Species richness varied from 2.0-2.9 in the sites. Total species richness was significantly correlated with total relative abundance (p=0.001). The distribution,abundance and principal component analysis plot suggest that Glomus macrocarpum,G. multicaulis,G. constrictum and Acaulospora sp 1 were the most host preferred species which possibly may favour the host with proper nutrient acquisition and growth.