Board Thread:Skyrim/@comment-12323841-20130716084813/@comment-11425537-20130719020457

Not her father, but her mother's father was a dunmer that was using magicka to appear as a Breton/Dunmer hybrid.

So...Magic. Magic is totally the reason.

(For those curious; Karliah's mom was Dralsi Indoril, Dralsi is Queen Barenziah's daugther, Barenziah boinked a Drayven Indoril disguised via magicka as Jagar Tharn, which resulted in Dralsi.)