Our findings established a functional link between ARL13B and the IFT pathway via an ARL3 effector ODA16, explaining the essential and diverse roles of ARL13B in ciliary transport of both membrane proteins required for signaling and axonemal cargos important for motility and providing insights to the disease mechanisms of ARL13B-ARL3 in motile ciliopathies. Here, DAW1 is linked to ciliopathy.