By default root login is disabled in GUI mode. Followi following steps to enable root login in GUI mode in Fedora
Step 1) Take backup of file being modified
cp /etc/pam.d/gdm /etc/pam.d/gdm.bk
Step 2) Open /etc/pam.d/gdm in your favorit editor
vi /etc/pam.d/gdm
Step 3) Comment following line in
#pam_succeed_if.so user != root quiet
Step 4) Save and close the file
Step 5) now take backup of gdm-password file
cp /etc/pam.d/gdm-password /etc/pam.d/gdm-password.bk
Step 6) open gdm-password file
vi /etc/pam.d/gdm-password
Step 7) Comment following line in gdm-password
#pam_succeed_if.so user != root quiet
Step 8) Save and close the file
If you are using Fingerprint auth mode, do following also
Step 1) now take backup of gdm-fintergprint file
cp /etc/pam.d/gdm-fintergprint /etc/pam.d/gdm-fintergprint .bk
Step 6) open gdm-password file
vi /etc/pam.d/gdm-fintergprint
Step 7) Comment following line in gdm-fintergprint
#pam_succeed_if.so user != root quiet
Step 8) Save and close the file