GenericsBaseInterface.cs

static void Main(string[] args)
{
  Mapper.Initialize(cfg =>
  {
  	  cfg.CreateMap<IBaseUserDto, IBaseUserEntity>()
          .ForMember(d=>d.Name, opt => opt.Ignore());
  
      cfg.CreateMap(typeof(BaseUserDto<>), typeof(BaseUserEntity<>));

      cfg.CreateMap(typeof(ConcreteUserDto), typeof(ConcreteUserEntity))
		  .IncludeBase(typeof(IBaseUserDto), typeof(IBaseUserEntity));
  });

  var user = new ConcreteUserDto
  {
      Id = "my-id",
      Name = "my-User"
  };

  var userEntity = Mapper.Map<ConcreteUserEntity>(user).Dump();
}

public interface IBaseUserDto
{
	string Name { get; set; }
}

public abstract class BaseUserDto<TIdType> : IBaseUserDto
{
   public TIdType Id { get; set; }
   public string Name { get; set; }
}

public class ConcreteUserDto : BaseUserDto<string>
{
}

public interface IBaseUserEntity
{
	string Name { get; set; }
}

public abstract class BaseUserEntity<TIdType> : IBaseUserEntity
{
   public TIdType Id { get; set; }
   public string Name { get; set; }
}

public class ConcreteUserEntity : BaseUserEntity<string>
{
}