Previous studies have documented that motor training improves performance on motor skill tasks and related this to altered functional brain activity in cerebellum, striatum, and frontal motor cortical areas. Mental training can also improve the performance on motor tasks, but the neural basis of such facilitation is unclear. The purpose of the present study was to identify neural correlates of training-related changes on a finger-tapping task. Subjects were scanned twice, 1 week apart, with fMRI while they performed two finger-tapping sequences with the left hand. In-between scans, they practiced daily on one of the sequences. Half of the participants received motor training and the other half received mental training (motor imagery). Both training procedures led to significant increases in tapping performance. This was seen for both the trained and the untrained sequence (non-specific effect), although the gain was larger for the trained sequence (sequence-specific effect). The non-specific training effect corresponded to a reduction in the number of activated areas from an extensive set of brain regions prior to training to mainly motor cortex and cerebellum after training. The sequence-specific training effect involved the supplementary motor area and the cerebellum for motor training and visual association cortex for mental training. We conclude that gains following motor and mental training are based on distinct neuroplastic changes in the brain.