In the present study, fungal flora from families Aleyrodidae, Aphididae and Coccidae of the order Hemiptera, suborder Sternorrhyncha, were isolatedfrom three different agroecological zones of Pakistan. Fusarium equiseti, Fusarium solani, Fusarium incarnatum and Fusarium sp. along with other fungi were isolated and characterized morphologically as well as genetically by amplifying internal transcribed spacer region (ITS). Variability among Fusarium species based on ITS showed that it is not enough to score diversity within species and isolates. Additionally pathogenicity of isolated Fusarium species was evaluated against nymph and adult of Bemisia tabaci. Under controlled conditions different species of Fusarium restrained the growth of B. tabaci as compared with control.