The Kookhittaan clan is generally considered to be an offshoot of the Ganaxtedi clan. McClellan quotes one informant from Teslin who says that ancestors of the Kookhittaan were supposed to have gone down the Taku River long before there were any other Tlingit speakers in the area. (The implication is that they were then Athabascan speakers). Another story says that the Kookhittaan are part of the Kaagwaantaan clan, which is part of the wolf moiety. The Kaagwaantaan claim to be the oldest and most powerful.
Another informant of McClellan's said that the name Kookhittaan was taken by a branch of the Ganaxtedi after some of the group had moved to Angoon. There the group split because there were too many Ganaxtedi living in one house. The new group built another house at the end of the village. But because they were afraid of the Ganaxtedi, they built a hole or cellar in the middle of the house in which to hide. Then name Kookhittaan means "people of the house with the hole in the middle". Another story says that they put the hole in the middle to protect the women and children of the house.
McClellan says that in the late 1800's or early 1900's, a potlatch house was built near the head of the Taku River, which had a large cellar dug out.
The clan emblem of the Kookhittaan is a crow with the three babies(sometimes carrying two human heads said to belong to slaves). They also use the Three-heads encircling the Salmon called Ick a taxt, (they represent spirits associated with the Salmon Hole of the Ishkahittaan people).