In this paper, we present a novel approach to enhance hierarchical phrase-based machine translation systems with linguistically motivated syntactic features. Rather than directly using treebank categories as in previous studies, we learn a set of linguistically-guided latent syntactic categories automatically from a source-side parsed, word-aligned parallel corpus, based on the hierarchical structure among phrase pairs as well as the syntactic structure of the source side. In our model, each X nonterminal in a SCFG rule is decorated with a real-valued feature vector computed based on its distribution of latent syntactic categories. These feature vectors are utilized at decoding time to measure the similarity between the syntactic analysis of the source side and the syntax of the SCFG rules that are applied to derive translations. Our approach maintains the advantages of hierarchical phrase-based translation systems while at the same time naturally incorporates soft syntactic constraints.