The Western Ghats of India is the one of the world's 10 "Hottest biodiversity hotspots" that runs along the western part of India through four states including Tamil Nadu. The only biodiversity reserve in the Western Ghats is the Nilgiri biosphere located in the Tamil Nadu state. In the present study, 525 soil samples were collected from all the 14 different divisions of the Western Ghats in Tamil Nadu state, India. A total of 316 new isolates of Bacillus thuringiensis (Bt) that produce parasporal crystalline inclusions were isolated from 525 soil samples. Seven different types of crystalline inclusions were observed in the 316 new isolates of Bt. Cuboidal inclusion was predominantly present in 26.9% of the Bt isolates when compared to other shapes. Further characterization of 70 of the 316 Bt isolates for crystal protein profile through SDS-PAGE revealed six different types of crystal protein profile viz., 135 and 65, 135, 95, 65, 43, and 30 kDa crystal proteins. Variation in the mass of crystal protein(s) purified from the isolates of Bt revealed molecular diversity of this bacterium prevalent in the Western Ghats of Tamil Nadu, India.