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Manifold alignment has been found to be useful in many areas of machine learning and data mining. In this paper we introduce a novel manifold alignment approach, which differs from “semisupervised alignment” and “Procrustes alignment” in that it does not require predetermining correspondences. Our approach learns a projection that maps data instances (from two different spaces) to a lower dimensional space simultaneously matching the local geometry and preserving the neighborhood relationship within each set. This approach also builds connections between spaces defined by different features and makes direct knowledge transfer possible. The performance of our algorithm is demonstrated and validated in a series of carefully designed experiments in information retrieval and bioinformatics.