The cytoskeleton globally reorganizes between mitosis (M-phase) and cytokinesis (C-phase), which presumably requires extensive regulatory changes. To reveal these, we undertook a comparative proteomic analysis of cells tightly drug-synchronized in each phase. We identified 25 proteins that bind selectively to microtubules in C-phase, and identified several novel binding partners including NUSAP. C-phase selective microtubule binding of many of these proteins depended on activity of Aurora kinases, as assayed by treatment with the drug VX680. Aurora-B binding partners switched dramatically between M-phase to C-phase, and we identified several novel C-phase selective Aurora B binding partners including PRC1, KIF4 and APC/C. Our approach can be extended to other cellular compartments and cell states, and our data provide the first broad biochemical framework for understanding C-phase. Concretely, we report a central role for Aurora-B in regulating the C-phase cytoskeleton.