There are 6 books in the Witches of Eileanan series. The newest book is The Fathomless Caves which came out in 2002.

Named Best First Novel by Locus

'Twas a time when dragons left their lair and evil shadowed the land....

On the Day of Reckoning, the witches of Eileanan were outlawed--and violations of the new order were punishable by death. Eileanan's Great Towers, once meccas of magic and learning, were left…
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2
The Pool of Two Moons

Book cover of The Pool of Two Moons
It has been 16 years since the Day of Reckoning, when magic and witchcraft were outlawed throughout all of Eileanan. And though rumors say that she is dead, the Arch-Sorceress Meghan of the Beasts still lives. Traveling with her are the true heir to the throne and the red-haired warrior…

3
The Cursed Towers

Book cover of The Cursed Towers
A new age dawns in the kingdom of Eileanan, but not without resistance. Now the Righ, Lachlan the Winged, overturns his dead brother’s decrees against witchcraft. But sixteen years of hatred and superstition have cloaked Eileanan in darkness. And though he has won the power of the Lodestar, Lachlan’s rule…

4
The Forbidden Land

Book cover of The Forbidden Land
After her adventures with the League of the Healing Hand, Finn the Cat finds her life at Castle Rurach boring. Snowbound for the winter and faced with the prospect of being molded into “Lady Fionnghal” by her mother, she pines to be on the battlefront with her father against the…

5
The Skull of the World

Book cover of The Skull of the World
In the land of Eileanan, the Pact of Peace has not meant the end of unrest. Isault and Lachlan must continue to deal with their military position in Tirsoilleir—where a spy has compromised their tactical secrets, leaving them at a tremendous loss.

Isabeau the witch longs to rejoin her sister…

6
The Fathomless Caves

Book cover of The Fathomless Caves
a I saw the scaly sea rise and flood the land, the Red Wanderer like a bloody gash in the sky. That is when they will come, with the rising o' the red comet the Fairgean shall come ...a Before his death, the blind prophet Jorge had foreseen the conjuring…