System.Data.SQLite is the official Nuget package from the SQLite maintainers. Generally speaking, System.Data.SQLite is more up-to-date with SQLite releases. Microsoft.Data.SQLite was designed to be a lightweight data provider for use with .Net Core. As of this writing, System.Data.SQLite (1.0.113.1) is based on the 3.32.1 release of SQLite while Microsoft.Data.SQLite (3.1.7) is based on the 3.28.0 release of SQLite. For more information see: https://docs.microsoft.com/en-us/dotnet/standard/data/sqlite/compare