Diversity within the entomopathogenic fungi have been traditionally analyzed using morphological features but morphology alone can lead to ambiguity pertaining to identification at species level. Therefore utilization of molecular methods to detect the level of polymorphism among species helps minimize the problem. Nine isolates of Metarhizium were morphologically characterized by assessing their colour, media pigmentation, size and shape of conidia. Molecular characterization was carried out by random amplified polymorphic DNA analysis. The RAPD - PCR assay for nine isolates were performed by amplifying random sequences using three RAPD primers. The amplification products for the different isolates were compared with each other and were screened for the presence or absence of specific bands. The scored band data was subjected to cluster analysis. A genetic similarity matrix was constructed using Jaccard’s coefficient method. Colony colour varied from pale green to blackish green. Pigment production was observed for four isolates. Average width of spores ranged from 2.10 - 4.10μm and length 3.20 - 7.69 μm. The spores were grouped as either oval, round or elongated. The three primers generated a total of 166 reproducible distinct bands among the 9 isolates and the similarity was estimated on the basis of number of shared bands. The Jaccard’s similarity coefficient between isolate pairs ranged from 0.00 to 0.70 indicating a high genetic diversity. The maximum similarity was noticed between isolates MIS13 and MIS18. A dendrogram was generated from RAPD patterns of the Metarhizium isolates. Grouping of isolates into clusters correlated with similarities in their RAPD DNA patterns.