Connect to database(mySQL) in a secure way?

[Kay Tracid]

Hi,
I want to connect to a mySQL database. mySQL has a database with a table for the users, whose have access to mySQL.
I created a database for my program with a table for the content and a table for allowed users.
If I connect, I have to use the user and password from the mySQL user table. I have to store this user name in my program. If sombody read this user, he had the permission to make a SELECT on my database for users and the content.
Is there a way to connect with using my user table? Or is there a other way?
please help...
Thanks a lot!