We used functional magnetic resonance imaging to investigate if different brain regions are controlling the temporal and ordinal structure of movement sequences during performance. Human subjects performed overlearned spatiotemporal sequences of key-presses using the right index finger. Under different conditions, the temporal and the ordinal structure of the sequences were varied systematically in relation to each other, using a factorial design: COMBINED had a rhythm of eight temporal intervals and a serial order of eight keys; TEMPORAL had an eight-interval rhythm produced on one key; ORDINAL had an isochronous rhythm and an eight-key serial order; two control conditions had an isochronous pulse performed on one or two keys, respectively. Brain regions involved in rhythmic and ordinal control of the sequences were revealed by analysing main effect contrasts for the corresponding factors. TEMPORAL and ORDINAL were also compared directly to test for significant differences. A dissociation was found between largely the presupplementary motor area, the right inferior frontal gyrus and precentral sulcus, and the bilateral superior temporal gyri, involved in temporal control, and lateral fronto-parietal areas, the basal ganglia and the cerebellum, which were implicated in ordinal control. The vermis and the superior colliculus were the only regions with an activity increase specifically related to combining long temporal and ordinal sequences. We conclude that humans use different brain networks for temporal and ordinal sequence control, and that the performance of combined sequences activates both networks, the medial cerebellum, and the superior colliculus.