This article examines the development of strain-specific sequence-characterized amplified region (SCAR) molecular markers in two strains of Beauveria bassiana and Metarhizium anisopliae, as well as their use for tracking pathogens in coinfected insect pests. The markers were designed based on the polymorphic introns of the large subunit region of the ribosomal DNA. These markers were used to distinguish between two strains of Beauveria (B55 and B51) and two strains of Metarhizium (M20 and M48). The entomopathogenic strains demonstrated synergistic increase in mortality against Spodoptera litura (Fabricius) (Lepidoptera: Noctuidae) larvae when infected with the coformulated M. anisopliae strain M20 + B. bassiana strain B55, particularly at a 2:1 proportion of LC50 concentration. The study revealed a disparity between intergeneric and interstrain coformulations. In intergeneric coformulations, one strain appeared predominant over the other strain at 1:2 and 1:4 proportions, both under in vivo and in vitro conditions. On the other hand, in interstrain coformulations, both strains survived and formed heterokaryons. Molecular studies revealed that the heterokaryons were unstable and reverted back to any one of the parent strains after 3 or 4 generations.