Plant chemistry can strongly influence interactions between herbivores and their natural enemies, either by providing volatile compounds that serve as foraging cues for parasitoids or predators, or by affecting the quality of herbivores as hosts or prey. Through these effects plants may influence parasitoid population genetic structure. We tested for a possible specialization on specific crop plants in Chelonus insularis and Campoletis sonorensis, two primary parasitoids of the fall armyworm, Spodoptera frugiperda. Throughout Mexico, S. frugiperda larvae were collected from their main host plants, maize and sorghum and parasitoids that emerged from the larvae were used for subsequent comparison by molecular analysis. Genetic variation at eight and 11 microsatellites were respectively assayed for C. insularis and C. sonorensis to examine isolation by distance, host plant and regional effects. Kinship analyses were also performed to assess female migration among host-plants. The analyses showed considerable within population variation and revealed a significant regional effect. No effect of host plant on population structure of either of the two parasitoid species was found. Isolation by distance was observed at the individual level, but not at the population level. Kinship analyses revealed significantly more genetically related—or kin—individuals on the same plant species than on different plant species, suggesting that locally, mothers preferentially stay on the same plant species. Although the standard population genetics parameters showed no effect of plant species on population structure, the kinship analyses revealed that mothers exhibit plant species fidelity, which may speed up divergence if adaptation were to occur.