Abstract: A set of Bt strains isolated from insects and soil samples, selected from different ecosystems in Kyrgyzstan was molecular taxonomically characterized using the pycA gene as marker for phylogenetic reconstruction. Within the Bacillus cereus sensu lato species complex, all Kyrgyz isolates were shown to belong to the B. cereus subspecies thuringiensis. Most isolates were assigned to the lineage Bt tolworthi, with two isolates each belonging to the lineages Bt kurstaki and Bt sotto. Targeted amplification of different cry gene variants revealed differences in cry gene frequencies. Whereas cry1 and cry4 genes were regularly detected, cry3 genes were identified in only a small number of Bt strains. Interestingly, the combination of cry1 and cry4 genes in the same strain was frequent, whereas the combination of cry1 and cry3 occurred only in a single Bt strain.