The human oral microbiome is associated with chronic diseases including cancer. However, our understanding of its relationship with diet is limited. We assessed the associations between carbohydrate and glycemic index (GI) with oral microbiome composition in 834 nondiabetic subjects from the NCI Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial and the American Cancer Society Cancer Prevention Study II cohorts. The oral microbiome was characterized using 16Sv3-4 rRNA sequencing from oral mouthwash samples. Daily carbohydrate and GI were assessed from food frequency questionnaires. We used linear regression, permutational multivariate ANOVA, and negative binomial Generalized Linear Models (GLM) to test associations of diet with α- and β-diversity and taxon abundance (adjusting for age, sex, cohort, body mass index, smoking, caloric intake, and alcohol). A q-value (FDR-adjusted P value) of <0.05 was considered significant. Oral bacterial α-diversity trended higher in participants in the highest quintiles of carbohydrate intake, with marginally increased richness and Shannon diversity (Ptrend = 0.06 and 0.07). Greater carbohydrate intake was associated with greater abundance of class Fusobacteriia (q = 0.02) and genus Leptotrichia (q = 0.01) and with lesser abundance of an Actinomyces operational taxonomic unit (q = 4.7E-04). Higher GI was significantly related to greater abundance of genus Gemella (q = 0.001). This large, nationwide study provides evidence that diets high in carbohydrates and GI may influence the oral microbiome. Significance: Taxonomic differences at the highest intake quintiles may reflect diet-induced increases in carcinogenic bacteria and decreases in protective bacteria. Genus Leptotrichia has been implicated in cancer and inflammatory disease, while immunostimulatory genus Gemella may increase inflammatory disease risk. These differences further our understanding of possible mechanisms leading to oral and systemic disease.