I am assuming that your server is connected directly to the Internet. The first question you need to ask is does your MySQL database server need to be accessed from the Internet or if you have a web server on the same machine and are accessing the database it via PHP? If everything is accessible locally then I would configure the firewall to block the MySQL port (default 3306). However, if your machine has been compromised the hackers may have made backdoors to get in. In which case you should back up everything and re-install a clean server but look very closely at how this is configured. Block all ports that are not needed from being accessed from the Internet (public ip address) and allow only access from local ip addresses.