LSSP-PCR (low stringency specific primer-PCR), technique was standardized for polymorphisms in native isolates cry1B genes Bacillus thuringiensis (Bt) identify. 164 isolates were evaluated by identifying the gene colombian native cry1Ba, in 11 of these isolates. The 11 amplified fragments, along with the reference strain Bt subsp. aizawai HD137 were analyzed by LSSP-PCR and electrophoretic patterns obtained were compared qualitatively. With the amplified products with direct oligonucleotide was constructed using UPGMA dendrogram showed three clusters with similarity of 83, 79 and 68%. The group with 68% similarity corresponded to the isolation BtGC120 native who introduced the variable pattern of bands. With the isolation BtGC120 reverse oligonucleotide showed less variability (43%). The nucleotide sequence obtained from this fragment of 806 bp showed 93% identity with the sequence of the genes of Bt morrisoni cry1Bc1 and cry1Bb1 BT-strain EG5847. Predicted reading frame of 268 +3 a protein amino acid residues with 88% identity with the protein Cry1Bc. This sequence revealed two domains, an N endotoxin involved in the formation of the pore and other related M endotoxin in re