Effect of disturbance on root colonization and vertical distribution of arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) was investigated at two adjacent sites of Lal Suhanra Biosphere Reserve, Pakistan. Disturbance clearly affected AMF and DSE colonization, vertical distribution of AMF and plant community structure. Mean colonization of AMF and DSE was slightly less at the disturbed site. Average spore densities, diversity and richness of AMF and DSE were higher at the undisturbed site. A study of the vertical distribution of AMF associated with the five plant species most common to each study site indicated that beside AMF and DSE colonization disturbance may affect AMF species composition. Correlation of AMF with DSE is also discussed.