This study determined the genetic similarity of 22 isolates of Metarhizium anisopliae and 51 isolates of Isaria amoenerosea isolated from mineral and peat soils, involving random amplified polymorphic DNA (RAPD) and using polymerase chain reaction (PCR) technology. The pathogenicity of the selected isolates from both genera of fungi were then tested against the subterranean termites, Coptotermes curvignathus. The RAPD-PCR analysis revealed high genetic similarity within the isolates of M. anisopliae and I. amoenerosea, at the similarity ranging from 52% to 100%. For M. anisopliae, the fungal isolates were grouped into two main clusters and the isolates of I. amoenerosea were separated into five main clusters. Within clusters in each species, there was little evidence on high similarity within isolates from the same soil type, but most of fungal isolates were well distributed within the clusters. Based on the bioassay data, the isolates of M. anisopliae were more pathogenic on termites, as compared to the isolates of I. amoenerosea. The isolates of M. anisopliae caused high percentage of infections, ranging from 71% to 84% at 15 days after treatment (DAT), and the isolate of M11H was the most pathogenic against termites with the LT50 value of 6.36 days. For isolates of I. amoenerosea, the percentage of infection were low, ranging from only 5% to 31%. This laboratory study showed that M. anisopliae has a potential to be used to control termites, as it has rapid infecting capability. However, further studies should be conducted to confirm the effectiveness of the M. anisopliae to control termites, especially in the field.