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Solution

1. Log-in to your server by SSH and switch to superuser mode.

2. Stop the MySQL service mysqld.

FreeBSD:
/usr/local/etc/rc.d/mysql-server stop

Linux:
service mysqld stop

3. Restart the service manually, but add the "--skip-grant-tables" parameter, e.g.

/bin/sh /usr/bin/mysqld_safe --datadir=/var/lib/mysql --socket=/var/lib/mysql/mysql.sock --pid-file=/var/run/mysqld/mysqld.pid --basedir=/usr --user=mysql --skip-grant-tables --user=root

The SSH might not return to the shell prompt, because I/O is redirected by MySQL. Simply close the SSH connection and open a new one, log in again and switch to superuser mode.

4. Log-in to the MySQL console without password:

mysql -u root

5. Set a new password with this SQL command:

UPDATE mysql.user SET password=PASSWORD('[new password]') WHERE user='root';
FLUSH PRIVILEGES;

Instead of [new password] enter a password of your choice. Special characters may lead to problems later on. It is often better to omit them.

6. Leave the MySQL console:

exit;

7. Stop the MySQL service mysqld once again:

FreeBSD:
/usr/local/etc/rc.d/mysql-server stop

Linux:
service mysqld stop

8. Restart the service manually, but this time omit the "--skip-grant-tables" parameter. It may be best to use the simplified start command:

FreeBSD:
/usr/local/etc/rc.d/mysql-server start

Linux:
service mysqld start

The new root password is now active.

Overview of frequently asked questions