Your mysql server has a normal root user as any mysql server, ispconfig does not change anything in this regard. If I installed the server for you, then you either received the mysql root password from me by email (please see my mail with the login detail that you received after the installation) or if mysql was already installed, then the mysql root password is the one that you sent me to install ispconfig.
You can also find the mysql root password that was working at the time ispconfig was installed in the file /usr/local/ispconfig/server/lib/mysql_clientdb.conf. If the password in that file does not work anymore, then either mysql is broken or you changed the password in the meantime.
The ISPConfig FAQ also contains instructions on how to reset a mysql root password:
If this wont work, then your mysql database is most likely broken by the mysql update. Do you have any server backups that you can restore?