It produces parasporal crystalline inclusions of various shapes such as bipyramidal, cuboidal, rectangular, spherical, and spore attached crystals during sporulation . It is a well established fact that cry1 and cry9 genes encode proteins of 130–135 sizes and cry2 encodes a protein of 60–70 kDa which are lepidopteran active In the present study a lepidopteran active Bt strain SWK1 isolated from spider web collected at Valley Kashmir situ- ated in northern western tip of Himalayan biodiversity hotspot was further characterized. The SEM analysis of spore crystal mix- ture revealed the presence of spherical and bipyramidal crystals. The spore crystal mixture of Bt isolate SWK1 when analyzed by SDS-PAGE exhibited two major protein bands with molecular masses of approximately 135 and 70 kDa as in the case of HD1 indicating the presence of lepidopteran active cry1 and cry2 genes. PCR analysis with cry2Aa specific primer resulted in the amplifica- tion of 498 bp. However when full ORF was amplified, sequenced and digested in silico and in vitro, it showed difference from other reported cry2A crystal protein genes. These results suggested that the isolate carried some cry2A related gene but not the cry2Aa gene. The sequence was named as cry2Al1, a new cry2A haplotype, by B. thuringiensis delta-endotoxin nomenclature committee.