This research aims to analyze the level of similarity and diversity among local isolates of B. thuringiensis Auky Island Padaido District in Biak Numfor Regency with NCBI gene bank base, the basis of which is to obtain B. thuringiensis isolates from jayapura local isolates that can act as controllers of Anopheles mosquito larvae. Several steps in the research are 16s gene amplification, PCR product purification, cloning using pTA2 vectors and transformation into competent E. coli Zymo 5α cells, confirmation with PCR colonies, recombinant plasmid isolation, sequencing analysis and phylogenetic tree construction. The isolates of ABNP8, ABNP9, ABNP11, ABNP12 and ABNP18 have been detected as local isolates from in Auky Island Padaido District in Biak Numfor Papua Regency that have great potential as bioinsecticides, and capable of controlling and killing Anopheles mosquito larvae. Of the five isolates, ABNP8 isolates had unique diversity and characteristics and were different from the four other isolates. Based on the similarity analysis in the MEGA7 program, the similarity rate reached 84%. Its diversity can be seen from the uniqueness of the sequence and its position in different branching dendrograms.