The invention discloses a method for separating and identifying pathogenic bacteria of insects, relating to the field of research for bacterial diseases of insects. The method comprises the followingsteps: S1, disinfecting the body surfaces of the insects carrying pathogenic bacteria, extracting hemolymph, carrying out diluting till the suitable concentration is achieved, coating an LB plate withthe diluent, carrying out culturing, picking out single colonies, thus obtaining pathogenic bacteria, carrying out pure culturing, transferring to liquid LB culture medium, and observing the morphological features of isolated strains under an oil immersion lens; S2, treating the thallus obtained by culturing in S1 by using lysozyme and SDS in sequence, and after the thallus is crushed, purifyingthe total DNA of the isolated strains through phenol extraction; and S3, amplifying the 16S rDNA with overall length of the isolated strains, after sequencing, carrying out clustering analysis, and determining the species of the isolated strain in combination with the morphological features of an isolated strain. The method for separating and identifying pathogenic bacteria of insects is universalfor gram-positive bacteria and gram-negative bacteria, and is suitable for separating and identifying pathogenic bacteria of the insects including bees, cotton bollworms, inchworms, Bombyx mori and the like, and the screened 16S rDNA amplification and sequencing primers are good in universality and high in stability.