Hive Queens are the source of all the hive bots, every system has one, it's just a matter of finding it. They are heavily guarded by Overseers, Guardians, Transports, and Assaults. The Hive Queens themselves are armed with a Frigate Gun, which is similar to a Gatling Turret. However, the Frigate Gun is several times more powerful, is faster, and has better auto-aim. This gun was originally mounted on the Frigate and can kill a fighter in two or three shots.
Killing a Hive Queen will not only give you thousands of experience points, but will also give you credit towards a Queen Hunter Badge, which entitles you to a special reward weapon (Mega Positron Blaster).
Hive Queens will most likely be gaining new features in the near future, and already are beginning to launch attacks on occupied sectors.