The soybean caterpillar Anticarsia gemmatalis (Lepidoptera: Noctuidae) is the main pest of the soybean crop. To control this pest, techniques have been used such as biological control based on the nucleopolyhedrovirus (AgMNPV) and plant resistance with cultivars that have a complex of defense substances present in resistant genotypes. Flavonoids such as rutin and genistein can act on the formation of fatty acids through the hydrolysis of phospholipids in cell membranes. Apparently rutin and genistein inhibit digestion in insects and in A. gemmatalis larvae they have an antibiotic effect and reduce survival. Some studies have shown that rutin and genistein in A. gemmatalis larvae resistant to the AgMNPV virus have increased mortality compared to susceptible larvae. This study describes the comparative morphology of susceptible and resistant populations to AgMNPV using light and scanning microscopy and histochemical studies.