In their study of the giant component in inhomogeneous random graphs, Bollobás, Janson, and Riordan introduced a class of branching processes parametrized by a possibly unbounded graphon. We prove that the tree structures underlying two such branching processes have the same distributions if and only if the corresponding graphons are fractionally isomorphic, a notion introduced by Grebík and Rocha. A different class of branching processes was introduced by Hladký, Nachmias, and Tran in relation to uniform spanning trees in finite graphs approximating a given connected graphon. We prove that that the tree structures of two such branching processes have the same distributions if and only if the corresponding graphons are fractionally isomorphic up to scalar multiple. Combined with a recent result of Archer and Shalev, this implies that if uniform spanning trees of two dense graphs have a similar local structure, they have a similar scaling limit. As a side result we give a characterization of fractional isomorphism for graphs as well as graphons in terms of their connected components.