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Novel cry genes are potential candidates for resistance management strategies due to their different structure and mode of action. Therefore, it is desirable to clone and express novel cry genes from several novel isolates of Bacillus thuringiensis (Bt). Eight different Bt strains (namely ISI-IS8) were isolated from the desert part of Rajasthan and a simplified PCR method was developed for extensive analysis of cry and cyt genes in the native isolates. PCR results demonstrated that cry1 type genes (100%) were the most abundant genes in the indigenous Bt strains, followed by vip3A (87.5%), cry2 (75%), cry9 (62%), cry3 (50%), cur1 (37.5%), cry7-8 (37.5%), cry5,12 14, 21 (25%), cyt1 (25%), ciy4 (12.5%) and cyt2 (12.5%). Further, PCR with degenerate primers also showed the presence of cry type genes. The toxicological characterization of these novel cry genes will have huge importance in transgenic technology and will be useful in transgenesis of crop plants for better resistance management.