Seven Trichoderma sp. were collected from different locations of Uttar Pradesh, India for evaluating their bioefficiency by determining their genetic variations. PCR-based Inter Simple Sequence Regions (ISSR) Marker employing 6 primers produced 30 scorable bands out of which 27 bands were polymorphic. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s  genetic distance produced 2 main clusters (1 isolates in cluster 1 and 6 isolates in cluster 2). The result indicating their genetic diversity has opened new possibility of using the most efficient and more isolates of Trichoderma in the preparation of effective biopesticide.