Prebiotic carbohydrates rich diets have been shown to reduce obesity and related non-communicable diseases because of their positive influence on gastrointestinal health. The prevalence of obesity in the US is rising; in particular, southern United States obesity rates are higher than the national average of 30.2%. Strawberries and raspberries could provide food solutions to reduce obesities. Strawberry is an economically important crop in North Carolina and South Carolina, and interest in growing raspberries is rising. Major dietary sources of prebiotic carbohydrates are cereals, legumes, small fruits, and vegetables. Although prebiotic data for cereals and pulses are beginning to appear, data on small fruits including strawberries and raspberries are not yet available. The objectives of this study were to (1) determine the types and concentration of prebiotic carbohydrates including simple sugars, sugar alcohols, fructans, oligosaccharides, resistant starch, cellulose, and other dietary carbohydrates in spring grown strawberries from South Carolina commercial producers and fall grown raspberries from North Carolina State University raspberry breeding program, and (2) determine the effect of freezing and storage conditions on prebiotic carbohydrates profiles and their concentrations. A total of 31 strawberry and 11 raspberry samples prebiotic carbohydrates were analyzed using high performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD). Experimental design was a complete randomized design with three replicates. Our results clearly indicated that both strawberries and raspberries contain significant amounts of prebiotic carbohydrates, and a single serving (150g) of fresh strawberries or raspberries provide 5-10 grams of prebiotic carbohydrates. In addition, genetic and environmental variations were observed in strawberry and raspberry water-soluble carbohydrate concentrations providing opportunities to optimize sweetness and other fruit quality parameters. Overall, Carolina grown strawberries and raspberries are nutritionally significant source of prebiotic carbohydrates: thus, it may be possible to further enhance those carbohydrates through breeding and locational sourcing towards obesity reduction.