[Background] The LM1212 strain, a member of the insect pathogen bacterium Bacillus thuringiensis (Bt), has an unique cell differentiation phenotype that spores and crystals are produced in spore-forming cells and crystal-producing cells, respectively. Compared to the wild-type LM1212, the mutant strain LM1212-DB formed a reduced proportion of spore-forming cells and a higher proportion of crystal-producing cells, which provided an excellent experimental material for studying the mechanism of crystal-producing cell formation. [Objective] In this study, we tried to reveal the potential reason for the phenotypic difference between these two strains by investigating their genomic differences. [Methods] The whole genomes of the two strains were sequenced by using the single molecular real-time (SMRT) technology on the Pacific Bioscience (Pacbio) RS II sequencing platform. The differences in chromosome, plasmid, two-component system and insertion sequence between two strains were analyzed, and a phylogenetic tree based on a gene related to phenotypic characteristics was constructed. [Results] Genomic analysis showed that both strains contained abundant insertion sequences and two-component systems, suggesting that two strains were prone to rearrange genes for environmental adaptation. Fragment deletion within chromosome and plasmid, rearrangement and copy number variation for plasmid occurred in the mutant LM1212-DB. Some environmental stress response genes such as sigB and sporulation-related genes such as abrB were found to be absent and one copy number of plasmid carrying the transcription factor CpcR increased in the genome of LM1212-DB. The evolutionary analysis of CpcR indicated that the strain carrying the cpcR homologous gene also had a cell differentiation phenotype similar to that of LM1212. The deletion of these important functional genes and the decreasing of the copy number may be responsible for the phenotypic differences between the two strains. In addition, LM1212-DB lacked type I restriction-modification system, which might endow it a better exogenous DNA compatibility, compared to the wild-type strain LM1212. [Conclusion] Structural variation of chromosomes and plasmids lead to phenotypic differences between LM1212 and LM1212-DB, which would provide a clue for the study on differentiation mechanism of LM1212 cells.