Bacillus thuringiensis (B. t.) strains are important microorganism because they produced a large amount of δ-endotoxin protein per bacterial cell and their toxins are highly toxic to Lepidoptera, Coleoptera, and Diptera depending on B. t. To date, more than a hundred Cry proteins have been identified and classified into 195 holotypes, based on the amino acid sequence identity. The Cry proteins or cry genes from the Korean native B. t. isolates in this study were not identified yet. The electrospray ionization of quadrupole time of flight mass spectrometry (ESI Q-TOF MS) was used to get the internal amino acid sequences of the endotoxin-spore culture mixtures of B. t. isolates, for which polymerase chain reaction (PCR) techniques were unable to detect the cognate genes. Most of Cry proteins seperated, excized, and extracted from the one dimensional - polyacrylamide gel electrophoresis (1D-PAGE), instead of 2D-PAGE, were matched with protein databases using MS-MASCOT search program. The internal amino acid sequences which were submitted to protein BLAST (basic local alignment search tool) had partially homology with the Cry protein databases. Hence, present data strongly suggest that the de novo amino acid sequencing and ESI Q-TOF/MS analysis along with MASCOT search could be used as a simple and rapid method for detection of novel Cry toxins from B. t. isolates and identification of B. t. isolates.