Some systems set the hostname to the FQDN and others set it to just the unqualified host name. I know the current BIND FAQ recommends the FQDN, but most Solaris systems, for example, tend to use only the unqualified host name.

Regardless, the way around this is to first get the host's name (perhaps an FQDN, perhaps unaualified). Most systems support the Posix way to do this using uname(), but older BSD systems only provide gethostname(). Call gethostbyname() to find your IP address. Then take the IP address and call gethostbyaddr(). The h_name member of the hostent{} should then be your FQDN.