The 9V is input. The 5V is output, for connected devices that need 5V regulated.
Power. This can be a regulated +5V power source (e.g. from the +5V pin of the Mini USB Adapter or an Arduino NG) connected to the +5V pin of the Arduino Mini. Or, a +9V power source (e.g. a 9 volt battery) connected to the +9V pin of the Arduino Mini.