Developing appropriate control measures for the Mahogany shoot borer, Hypsipyla robusta Moore has become increasingly impor- tant due to the severe damaging effect of the pest on the establishment of the saplings of Swietenia mahagoni Jacq (Sapindales: Meliaceae). Exist- ing management methods are largely limited to silvicultural practices and spraying of chemical insecticides. To identify a potential fungal biocon- trol agent, we compared the virulence of six native and two standard ARSEF isolates of Metarhizium anisopliae Metsch. against this pest. The average survival time and conidial yield of IWST-Ma7 was higher (6.2 to 7.3 days and 4.9 to 4.7 × 105 conidia/ml) than the standards. Sig- nificant difference in sporulation on the cadavers between isolates, doses and incubation periods were substantiated for the selection of potential strain. The mycotoxic effects of crude soluble protein extract when in- corporated in the artificial diet, the ARSEF 2596 and ARSEF 3603 showed LD50 value of 3.7% and 5.6%. However, IWST-Ma7 was highly lethal with significant lowest LD50 value of 2.6%. The enzyme activity of IWST-Ma7 was highest for chitinase, CDA, protease and lipase viz., 1.90 U/mg, 1.80 U/mg, 0.98 U/mg and 0.80 U/mg respectively. However the enzyme activity of chitinase and Chitin deacetylase assay for all the isolates was significantly higher than protease and lipase activity. The ITS regions (5.8S rDNA and 28S rDNA) of seven isolates of M. Ani-sopliae were amplified using the ITS1 and ITS4 primers which was a unique fragment of approximately 550 bp. Based on ITS regions, phylogenetic tree have been constructed and the isolates have been grouped in to 5 clades. The virulence and mycotoxic effects of different isolates could rationally be used to employ them for the management of the mahogany borer.