The basilisk throne / Greg Keyes.

Enhanced descriptions from Syndetics:

Master and Commander meets A Game of Thrones and Pirates of the Carribean . Rapid-paced high fantasy with all-out combat on the high seas, and a canny young woman who faces the hidden threats of an imperial court. Yet the key to defeating a sorcerous enemy may lie with a wild rogue and the slave of a maniac.

For centuries the Drehhu have ruled every continent, brutally enslaving the human inhabitants. Now after endless wars the human empires of Ophion, Velesa, and Modjal have pushed the inhuman enemy back to their heartland and unite in a final, massive assault.

Alastor Nevelon and his son Crespin set sail against the Drehhu, and they have their own secret weapons. Yet Alastor is forced to send his daughter Chrysanthe to the capitol city Ophion Magne as a "token" of his loyalty to the emperor. He instructs Chrysanthe to use her considerable intellect to discover what plots may be afoot, even as she enters a place where courtly manners hide murderous intent.

As nations collide the true key to defeating the Drehhu may lie in a remote mountain stronghold, with a wild rogue known as Hound and Ammolite, the young slave of a sorcerer more ancient than any nation--whose loyalties remain threateningly unknown.