The gut microbiota plays important roles in the bioecology of insects, including host plant adaptation and speciation. Spodoptera frugiperda has two well-established host-adapted strains with marked differences at the genetic and host plant utilization levels. We investigated whether differences in the gut microbiota would occur between the “corn” ( CS ) and “rice” ( RS ) strains of S. frugiperda when feeding on different crops. The gut microbiota of larvae fed on corn and millet was predominantly represented by Firmicutes followed by Proteobacteria , with an opposite pattern in larvae fed on cotton. No differences were observed between the CS and RS using PERMANOVA. PCoA analyses resulted in distinct bacterial clusters based on the host plant. Comparisons of strains gut microbiota at the phylum level resulted in differences only for larvae fed on cotton, but differences in the relative abundance of minor representatives at the genus level between strains were observed regardless of the food source used. We also found differences in the potential functional contribution of bacteria between the strains. In conclusion the gut microbiota of S. frugiperda is strongly modulated by the host plant while strains seemed to play a minor role in changing the abundance of members of the gut bacterial community.