We give a notion of branching systems on ultragraphs. From this we build concrete representations of ultragraph C*-algebras on the bounded linear operators of Hilbert spaces. To each branching system of an ultragraph we describe the associated Perron-Frobenius operator in terms of the induced representation. We show that every permutative representation of an ultragraph C*-algebra is unitary equivalent to a representation arising from a branching system. We give a sufficient condition on ultragraphs such that a large class of representations of the C*-algebras of these ultragraphs is permutative. To give a sufficient condition on branching systems so that their induced representations are faithful we generalize Szymański's version of the Cuntz-Krieger uniqueness theorem for ultragraph C*-algebras.Ultragraphs are combinatorial objects that generalize directed graphs. Roughly speaking an ultragraph is a graph where the image of the range map does not belong to the set of vertices, but instead to the power set on vertices. The concept was introduced by Mark Tomforde in [24] with an eye towards C*-algebra applications. In particular, Tomforde showed in [24] how to associate a C*-algebra to an ultragraph and proved that there exist ultragraph C*-algebras that are neither Exel-Laca algebras nor graph C*-algebras. So the study of ultragraph C*-algebras is of interest, but furthermore, ultragraph C*-algebras were key in answering the long-standing question of whether an Exel-Laca algebra is Morita equivalent to a graph algebra (see [16]).Recently the scope of ultragraphs has surpassed the realm of C*-algebras, reaching applications to symbolic dynamics. In particular, ultragraphs are fundamental in characterizing one-sided shift spaces over infinite alphabets. Furthermore, questions regarding the dynamics of one-sided shift spaces over infinite alphabets were answered using ultragraphs and their C*-algebras (see [13]).The above evidence leads us to believe that there are still many applications of ultragraphs to be found. Indeed, among the results we present in this paper, we will show a connection (via branching systems) between ultragraphs and the Perron-Frobenius operator from the ergodic theory (see Section 5), therefore generalizing results previously obtained for graph algebras and Cuntz-Krieger C*-algebras (see [10,12]).Branching systems are not just important as a way to connect ultragraphs to the ergodic theory. They have appeared in fields as random walks, symbolic dynamics, wavelet theory and are strongly connected to the representation theory of combinatorial algebras. In particular, Bratteli and Jorgensen have initiated the study of wavelets and representations of the Cuntz algebra via branching systems in [3,4]. After this, many results relating branching systems and representations of generalized Cuntz algebras were obtained, see