We propose a new unsupervised algorithm for the automatic alignment of two manifolds of different datasets with possibly different dimensionalities. Alignment is performed automatically without any assumptions on the correspondences between the two manifolds. The proposed algorithm automatically establishes an initial set of sparse correspondences between the two datasets by matching their underlying manifold structures. Local feature histograms are extracted at each point of the manifolds and matched using a robust algorithm to find the initial correspondences. Based on these sparse correspondences, an embedding space is estimated where the distance between the two manifolds is minimized while maximally retaining the original structure of ...