Lichen thallus, composed of photobiont, mycobiont and often other fungi and bacteria, can be considered as mini-ecosystem comprising several organisms. The present study was focused on the isolation and identification of the fungusassociated with the corticolous lichen Flavoparmelia caperata collected from subalpine forest of Cedar (Cedrusdeodara (Roxb.) G. Don) in Chakrata district, Uttarakhand, India; comparison of secondary metabolites produced from the isolated fungus and the lichen thallus via Thin Layer Chromatography; and examining the host range or habitats of isolated fungus via studying the effect of natural selection on molecular polymorphism (Tajima's neutral theory of melocular evolution) in isolated fungus population. The fungus was isolated through whole tissue culture method on Potato Dextrose Agar (PDA) medium and identified morphologically and molecularly. Results suggested that Beauveriaaff.bassiana, a soil borneentomopathogenic fungus, was associated with the lichen thallus and also produces certain compounds. The secondary metabolites produced in the lichen thallus wasa combinedproduct of lichenized fungus andthe isolated fungus. F. caperataacts as a host for B. aff.bassiana and the later associated with the thallus of former one produces secondary metabolites which might help in the antiherbivory and survival of lichen in forests. Due to the effect of natural selection, molecular polymorphism (Tajima's D value= -0.386) exhibited by the B. bassiana population across the globe explains the wide host range or habitats.