Both the USDA & the FNDDS databases are provided by the USDA.
The USDA SR (Standard Reference) database includes single ingredients, whole foods, some brand name items, & some prepared dishes. The FNDDS (Food & Nutrition Database for Dietary Studies) includes whole foods, some brand name items, & additional prepared dishes that you may not find in the USDA SR database.
The USDA SR database is used for the analyses of the FNDDS database foods, so both are based on the same data sets. There will be some duplicates, but the databases also compliment each other.
The USDA SR database reports over 100 nutrient fields (however data is not populated for all foods - some missing data). The FNDDS database reports about 60 nutrients (with the majority of these fields populated - very little missing data).
As a general rule of thumb, we suggest that you find the closest match to the food you need. If you see duplicates, use the USDA SR option first.