The novel serogroup of Bacillus thuringiensis serovar mogi (H3a3b3d) was isolated from fallen leaves, sampled in a forest region of the city of Mungyeong, Korea. Plasmids from B. thuringiensis have been implicated in pathogenicity as they carry the genes responsible for different types of diseases in mammals and insects. In this study, the genome sequence of the strain was determined. The 6.0-Mb genome of B. thuringiensis mogi contains three replicons: a circular chromosome (5.40-Mb) encoding 5,652 predicted open reading frames (ORFs), and two megaplasmids, pMOGI364 (364 564 bp) and pMOGI222 (222 348 bp). The G+C contents of these replicons ranged from 31.3% to 34.2% for pMOGI364 and pMOGI222, respectively. There are six putative cry genes, cry19Bb1, cry73Aa, cry20Bb1, cry27Ab1, cry4Aa and cry56Ba1, distributed on these two megaplasmids. To investigate the role of these genes in crystal production, the expression profiles of these toxin genes were analyzed by quantitative PCR (qPCR) from the wild type strain. Also, these cry genes were cloned to the Escherichia coli-B. thuringiensis shuttle vector, pHT1K under the control of its own promoter and then introduced into an acrystalliferous B. thuringiensis Cry-B strain for further molecular characterization.