remove phpmyadmin Centos 6.5

The easiest way would be to enable REMI and EPEL RHEL/CentOS/Fedora repository (REMI has recent version of PMA, EPEL provides missing dependencies)

rpm -Uvh http://rpms.famillecollet.com/enterprise/remi-release-6.rpm
rpm -Uvh http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm

and then to install the PMA package (current version in repo is 4.0.6)

yum --enablerepo=remi install phpmyadmin

What HTTP server do you have installed on that machine? With Apache you don’t need to setup any VirtualHost because you will get working PMA automatically. The main configuration file for Apache is located under /etc/httpd/conf.d/phpMyAdmin.conf. The PMA configuration file is in /etc/phpMyAdmin/config.inc.php.

Now, how to remote the old version? Do you install it as RPM package? Then try

yum remove phpmyadmin

If you installed it by hand, where is it installed? To uninstall it simply means to remove its directory. How do you access it? Are there any aliases to map e.g. http://www.yourserver.com/phpmyadmin to that directory? Then, undefine those aliases.