ASP.NET Web Application and MySQL with custom Identity Storage

Create a db in your MySql server with the required tables and follow these steps :

1. Import MySql.Web, MySql.Data and MySql.Data.Entity.EF6 dlls into your project first.
2. Now create a Entity framework data model from your database by right clicking any folder -> new item -> Data -> ADO.net entity data model
3. Click Generate from database -> Next
4. Click on New Connection -> Change ->
5. Select MySql Database as datasource
6. Give your MySql server credentials and select database to generate the data model from database

It should work fine.

Edit : You can also pass the name of the connection string (stored in the web.config) in your context to the base constructor of the IdentityDbContext

public class MyDbContext : IdentityDbContext<MyUser>
{
  public MyDbContext()
    : base("TheNameOfTheConnectionString")
  {

  }
}

Check this for more info