To every singular reduced projective curve X one can associate, following E. Esteves, many fine compactified Jacobians, depending on the choice of a polarization on X, each of which yields a modular compactification of a disjoint union of the generalized Jacobian of X. We prove that, for a reduced curve with locally planar singularities, the integral (or Fourier-Mukai) transform with kernel the Poincaré sheaf from the derived category of the generalized Jacobian of X to the derived category of any fine compactified Jacobian of X is fully faithful, generalizing a previous result of D. Arinkin in the case of integral curves. As a consequence, we prove that there is a canonical isomorphism (called autoduality) between the generalized Jacobian of X and the connected component of the identity of the Picard scheme of any fine compactified Jacobian of X and that algebraic equivalence and numerical equivalence of line bundles coincide on any fine compactified Jacobian, generalizing previous results of Arinkin, Esteves, Gagné, Kleiman, Rocha, Sawon.The paper contains an Appendix in which we explain how our work can be interpreted in view of the Langlands duality for the Higgs bundles as proposed by Donagi-Pantev.Key words and phrases. Compactified Jacobians, Fourier-Mukai transform, autoduality, Poincaré bundle, Abel map. 1 More generally, for an arbitrary abelian variety A with dual abelian variety A ∨ , Mukai proved that the Fourier-Mukai transform associated to the Poincaré line bundle on A × A ∨ gives an equivalence between the bounded derived category of A and that of A ∨ . 1 are separating nodes (e.g. nodal curves of compact type). Finally, while this paper was under the referee process, two related papers have appeared on arXiv: D. Arinkin and R. Fedorov established in [AF16] a partial Fourier-Mukai transform for degenerate abelian schemes (in characteristic zero); J. L. Kass proved in [Kas] that autoduality holds true for (possibly coarse) compactified Jacobians of nodal curves and stable quasiabelian varieties (in characteristic zero).The main motivation for this work comes from the Langlands duality conjecture for Hitchin systems proposed by Donagi-Pantev in [DP12] as a classical limit of the conjectural geometric Langlands correspondence (which we review in more details in the Appendix ). In the special case of the Langlands self-dual linear group GL r , the Langlands duality conjecture predicts an autoequivalence Φ :of the bounded derived category of quasi-coherent sheaves of the moduli stack M of Higgs bundles of rank r on a fixed smooth projective curve C, which should intertwine the classical limit tensorization functors with the classical limit Hecke functors (see [DP12, Sec. 2] for more details). The moduli stack M of Higgs bundles admits a morphism H : M → A, called the Hitchin morphism, to an affine space A parametrizing certain degree-r singular covers of C, called spectral curves (see (10.1)). According to the so-called spectral correspondence (see Fact 10.3), the fiber of H −1 ( C) over a given spect...