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Do they refer to the same thing or is root just a location in filesystem (its ultimate base) and superuser a privileged user (sort of equivalent of windows administrator account) ? Do they need the same password ? Is superuser the kernel itself?

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'root' is traditionally the name given to the user account with superuser level rights. In this respect they are one and the same, though there is no rule that I know of that says that the superuser account must be called root.

It may be that the account was named 'root' due in part to the fact that only the superuser has write permission to the root directory (/)

The Windows Administrator account is not analogous to the Unix superuser account since there are restrictions on what a Windows Administrator can do. The analog to root on Windows NT based OSes is the SYSTEM account, which cannot be used by an interactive user.

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The kernel identifies the root user by its uid (0). You can name that account whatever you like in /etc/passwd. Not having an account called root may confuse some of the system software, but you can have more entries; some paranoid people have a root entry and a toor entry in /etc/passwd, both with UID 0, but with different shells, so that if one of the shells was broken somehow (e.g. due to a disk error) the other one could be used to log in and repair the system. –  Gilles Apr 9 '11 at 10:37
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/ is the top level directory in linux.All the subdirectories is under the /. the /root is default home directory of root user.

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