Every ship has a unique serial number (SN), which is a case-sensitive seven-character identifier of the form XXabcde, where XX is a two-letter code uniquely identifying the owning empire, and abcde is a random and unique five-character string of hexadecimal digits.  The game server will automatically determine your empire's two-letter code based on its name, ensuring that all empire codes in the same game are unique.  For example, a ship owned by The_Culture might have the serial number TC5f09d. 
 
For convenience you may give your ships unique names, and you may refer to any ship by its handle, i.e., either its SN or its name.  Since two empires could have ships with the same name, referring to other empires' ships when submitting orders to the game server is a bit problematic.  The server will try to accommodate, and if it does not detect any ambiguousness in ship names within a given sector, the enemy's own name for the ship can be used.  Otherwise, the SN must be used to identify the ship you want to reference.