“Endosymbiosis” is a cohesive form of a symbiotic association. Endobacteria exist in many fungi and play important roles in fungal host biology. Metarhizium spp. are important entomopathogenic fungi for insect pest control. In the present study, we performed comprehensive analyses of strains of Metarhizium bibionidarum and M. anisopliae using PCR, phylogenetics, and fluorescent electron microscopy to identify endobacteria within hyphae and conidia. The results of the phylogenetic analysis based on 16S rRNA gene sequences indicated that these endobacteria were the most closely related to Pelomonas puraquae and affiliated with Betaproteobacteria. Ultrastructural observations indicated that endobacteria were coccoid and less than 500 nm in diameter. The basic characteristics of endobacteria in M. bibionidarum and M. anisopliae were elucidated, and biological questions were raised regarding their biological functions in the Metarhizium hosts.