The order Lepidoptera is one of the most important pests of cotton (Gossypium barbadens). These insects are controlled with synthetic insecticides, which contaminate the environment. Therefore, biological control is an environmentally friendly alternative to the use of such chemicals. The objective of this research was to isolate native strains of Bacillus thuringiensis (Bt) and evaluate their toxicity against Spodoptera frugiperda and Alabama argillacea, which are insect pests of the cotton crop. The native strains of Bt were isolated from soil samples from different cotton areas of the Piura, Perú. 600 colonies of the genus Bacillus were obtained, of which 37 native strains presented morphological characteristics similar to the standard strains of Bt (HD1 and NA118). The morphological and biochemical characterization showed that 15 strains showed parasporal crystal of bipyramidal form of toxic action against Lepidoptera, exhibiting biochemical characteristics equal to the standard strains of Bt. The toxic effect of these 15 native strains was evaluated through a food poisoned test using lettuce and cotton leaf discs. The results showed that strains IN-24, IN-30 and IN-34 caused 100% mortality in S. frugiperda; strains IN-19, IN-24 and IN-25 caused 100% mortality in A. argillacea; while strain IN-24 caused 100% mortality in both species. The artificial diet test showed that strains IN-34, IN-01 and IN-31 caused the highest mortality rates in S. frugiperda and A. argillacea, respectively, when compared with the standard strains HD1 and NA118. It is concluded that there are several native strains of B. thuringiensis that can control S. frugiperda and A. argillacea.