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