In order for root user to be able to login, first of all make sure it's listed in
AllowedUsers if this directive is being used.
Second, change
PermitRootLogin from yes/no to "without-password":
Code:
#PermitRootLogin yes
PermitRootLogin without-password
Quote:
PermitRootLogin
Specifies whether root can log in using ssh(1). The argument
must be ``yes'', ``without-password'', ``forced-commands-only'',
or ``no''. The default is ``no''. Note that if
ChallengeResponseAuthentication is ``yes'', the root user may be
allowed in with its password even if PermitRootLogin is set to
``without-password''.
If this option is set to ``without-password'', password authenti-
cation is disabled for root.
If this option is set to ``forced-commands-only'', root login
with public key authentication will be allowed, but only if the
command option has been specified (which may be useful for taking
remote backups even if root login is normally not allowed). All
other authentication methods are disabled for root.
If this option is set to ``no'', root is not allowed to log in.
Restart ssh daemon and try again (Leave one terminal up as backup).