Dynamics in animal-associated microbiota can be difficult to study due to community complexity. Previous work showed that microbial communities in the midguts of Pieris rapae larvae contain relatively few members. In this study, we used P. rapae to test hypotheses related to how diet impacts gastrointestinal microbiota. More specifically, we investigated how the concentration of sinigrin, a glucosinolate in the natural diet of this insect, alters microbial community structure. Larvae were fed either sterile wheat germ diet alone or amended with 3.0 mg/ml, 6.0 mg/ml, or 9.0 mg/ml of sinigrin. In order to determine shifts in the gut microbial community, 16S rRNA genes from midguts were subjected to pyrosequencing and analyzed. Sinigrin had a significant impact on microbial communities in fourth instar P. rapae larvae, but this was dependent on concentration. The predominant phyla in all treatment groups were Proteobacteria and Firmicutes. Significant difference in beta diversity was typically observed when sinigrin 6 mg/ml and the control treatment groups were compared. The impact of sinigrin on the structure of the midgut microbiota is dependent on concentration, but not in a linear fashion. This may indicate that types and concentrations of glucosinolates have varied impact on midgut microbial community.