Fix a squarefree integer N, divisible by an even number of primes, and let Γ′ be a congruence subgroup of level M, where M is prime to N. For each D dividing N and divisible by an even number of primes, the Shimura curve X D (Γ0(N/D) ∩ Γ′) associated to the indefinite quaternion algebra of discriminant D and Γ0(N/D) ∩ Γ′-level structure is well defined, and we can consider its Jacobian J D (Γ0(N/D) ∩ Γ′). Let J D denote the N/D-new subvariety of this Jacobian. By the Jacquet-Langlands correspondence [J-L] and Faltings’ isogeny theorem [Fa], there are Hecke-equivariant isogenies among the various varieties J D defined above. However, since the isomorphism of Jacquet-Langlands is noncanonical, this perspective gives no information about the isogenies so obtained beyond their existence. In this paper, we study maps between the varieties J D in terms of the maps they induce on the character groups of the tori corresponding to the mod p reductions of these varieties for p dividing N. Our characterization of such maps in these terms allows us to classify the possible kernels of maps from J D to J D′, for D dividing D′, up to support on a small finite set of maximal ideals of the Hecke algebra. This allows us to compute the Tate modules $$T_\mathfrak{m} $$ J D of J D at all non-Eisenstein $$\mathfrak{m}$$ of residue characteristic l > 3. These computations have implications for the multiplicities of irreducible Galois representations in the torsion of Jacobians of Shimura curves; one such consequence is a “multiplicity one” result for Jacobians of Shimura curves.