Tobin and Brother

In the kingdom of Skala, for fear of an ancient prophecy, King Erius had his femle relatives assassinated.
But his sister he spared, and the identity of her daughter was concealed at birth by dark magic. So she has her brother's appearance and sex, until she has the age to overthrow her uncle, the usurper. But, her twin brother, who was killed that she might be saved, still haunts her and wants she revenge him, for his murder.

Book: "Tamir Triad" by Lynn Flewelling.