A pebble tree is an ordered tree where each node receives some colored pebbles, in such a way that each unary node receives at least one pebble, and each subtree has either one more or as many leaves as pebbles of each color. We show that the contraction poset on pebble trees is isomorphic to the face poset of a convex polytope called pebble tree polytope. Beside providing intriguing generalizations of the classical permutahedra and associahedra, our motivation is that the faces of the pebble tree polytopes provide realizations as convex polytopes of all assocoipahedra constructed by K. Poirier and T. Tradler only as polytopal complexes.