A sensorimotor sequence may contain information structure at several different levels. In this study, we investigated the hypothesis that two dissociable processes are required for the learning of surface structure and abstract structure, respectively, of sensorimotor sequences. Surface structure is the simple serial order of the sequence elements, whereas abstract structure is defined by relationships between repeating sequence elements. Thus, sequences ABCBAC and DEFEDF have different surface structures but share a common abstract structure, 123213, and are therefore isomorphic. Our simulations of sequence learning performance in serial reaction time (SRT) tasks demonstrated that (1) an existing model of the primate fronto-striatal system is capable of learning surface structure but fails to learn abstract structure, which requires an additional capability, (2) surface and abstract structure can be learned independently by these independent processes, and (3) only abstract structure transfers to isomorphic sequences. We tested these predictions in human subjects. For a sequence with predictable surface and abstract structure, subjects in either explicit or implicit conditions learn the surface structure, but only explicit subjects learn and transfer the abstract structure. For sequences with only abstract structure, learning and transfer of this structure occurs only in the explicit group. These results are parallel to those from the simulations and support our dissociable process hypothesis. Based on the synthesis of the current simulation and empirical results with our previous neuropsychological findings, we propose a neuro-physiological basis for these dissociable processes: Surface structure can be learned by processes that operate under implicit conditions and rely on the fronto-striatal system, whereas learning abstract structure requires a more explicit activation of dissociable processes that rely on a distributed network that includes the left anterior cortex.