Inter-simple sequence repeat (ISSR) markers were used to investigate genetic diversity among 39 isolates of Beauveria spp. (36 B. bassiana, one B. brongniartii, one B. amorpha, and one B. velata) isolated from different insect hosts and geographical origins. Eighteen among 33 primers that contained different simple sequence repeats (SSR) were chosen for their reproducibility and high polymorphism. Considerable intraspecific and interspecific variability among the isolates of Beauveria spp. was revealed. One hundred sixty-eight highly reproducible fragments were amplified in all 39 isolates with an average of 9.3 markers per primer; among these, 161 (95.8%) were polymorphic. For 36 B. bassiana isolates, 8.9 (1–13) markers per primer were scored, and a total of 123 fragments were amplified, in which 102 (82.9%) were polymorphic. Among the 168 polymorphic bands, 7 bands were considered to be specific for B. brongniartii isolate Bbr06, 14 bands for B. amorpha isolate Ba08, and 18 bands for B. velata isolate Bv01. Within 36 B. bassiana isolates, genetic similarity ranged from 0.651 to 0.972. However, the genetic similarity values among different Beauveria species ranged from 0.411 to 0.720, suggesting that ISSR technique was successful in differentiating the three closely related species from B. bassiana. The results also indicated that there was a certain association between B. bassiana isolates and their geographical origins, but no clear correlation between those isolates and their insect hosts. The present study suggested that ISSR markers can be used as robust molecular markers for the population genetics, epidemiological and ecological studies of entomopathogenic fungi.