The group of isometries W of a regular rooted tree, and many of its subgroups with branching structure, have groups of automorphisms induced by conjugation in W. This fact has stimulated the computation of the group of automorphisms of such well-known examples as the group G studied by R. Grigorchuk, and the group H studied by N. Gupta and the second author. In this paper, we pursue the larger theme of towers of automorphisms of groups of tree isometries such as G and H. We describe this tower for all groups acting on the binary rooted tree which decompose as infinitely iterated wreath products. Furthermore, we describe fully the towers of G and H. More precisely, the tower of G is infinite countable, and the terms of the tower are 2-groups. Quotients of successive terms are infinite elementary abelian 2-groups. In contrast, the tower of H has length 2, and its terms are {2,3}-groups. We show that the quotient aut^2(H)/aut(H) is an elementary abelian 3-group of countably infinite rank, while aut^3(H)=aut^2(H).