Problem:
If you are using MySQL Server version 4.x.x on your server but when you try to access PHPMyAdmin from Cpanel you will get following Error:

phpMyAdmin – Error
You should upgrade to MySQL 5.0.15 or later.

Due to your application configuration or any other reason you want to access PHPMyAdmin without upgrading MySQL version to 5.x.

Solution:
To fix this issue you should have root level access to your Server (if you are on shared server please contact your hosting company).

1) Login to server (SSH) using root login credentials.
2) Remove “_usr_bin_mysql_config_–version” file using following command

root@server [~]# rm -f /root/.cpanel/datastore/_usr_bin_mysql_config_–version

3) Now update your PHPMyAdmin (forcefully) with following command

root@server [~]# /usr/local/cpanel/bin/updatephpmyadmin –force
patching file config.sample.inc.php
patching file db_operations.php
patching file libraries/auth/http.auth.lib.php
patching file libraries/common.inc.php
patching file libraries/db_links.inc.php
patching file libraries/navigation_header.inc.php
patching file libraries/session.inc.php
patching file main.php
patching file server_privileges.php
cPanel authentication library installed.
cPanel API interface library installed.
phpMyAdmin updated to 3.3.8.1-all-languages.cp5

Now try to access PHPMyAdmin