If Appearance settings are not visible on the main index.php page, then (as root) go to
/usr/share/phpmyadmin
There should be a dummy file config.sample.inc.php, rename it to config.inc.php.
Then simply change the theme with the dropdown option on main index.php page (Home).
Only root can do this (admin rights). Download a theme from official theme page or other sources and extract ZIP to /usr/share/phpmyadmin/themes.
Best dark theme: BooDark