Beauveria spp. (one Beauveria sp., two B. brongniartii, and 47 B. bassiana) isolated from insects and soil from Kenya and other 16 different countries, were obtained from the CABI Bioscience Genetic Resource Collection. DNA was extracted from the 50 isolates and their genetic variability was investigated using restriction analysis of the internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP), ITS sequencing, and amplified fragment length polymorphism (AFLP). The B. bassiana isolates could not be distinguished by ITS-RFLP as all of them showed the same banding pattern. However, the AFLP technique provided more information on polymorphism between the isolates, allowing them to be clustered by relative similarity using band matching and unweighted pair group method with arithmetic mean analysis. Although no significant correlation between the isolates and host and geographical origins were observed, the technique revealed clonal populations of B. bassiana within Kenya.