Separation of sister chromatids is a drastic and irreversible step in the cell cycle. The key biochemistry behind this event is the proteolysis mediated by the ubiquitin ligase called the anaphase promoting complex, or APC/C. Securin and cyclin B1 are the two established substrates for APC/ C whose degradation releases separase and inactivates cyclin B1-dependent kinase 1 (cdk1), respectively, at the metaphase-to-anaphase transition. In this study, we have combined biochemical quantifications with mathematical simulations to characterize the kinetic regulation of securin and cyclin B1, in the cytoplasmic and chromosomal compartments, and found that they are differentially distributed and degraded with different rates. Modeling their interaction with separase predicted that activation timing of separase well coincides with the decline of securin-separase concentration in the cytoplasm. Notably, it also coincides with the peak of cyclin B1-separase level on chromosomes, which appeared crucial to coordinate the timing for separase activation and cdk1 inhibition. We have also conducted phosphoproteomic analysis and identified Ki67 as a chromosomal cdk1 substrate whose dephosphorylation is facilitated by cyclin B1-separase interaction in anaphase.Mitosis is characterized by a synchronous separation of sister chromatids at anaphase onset. The anaphase events are induced by the action of the AnaphasePromoting Complex, or APC/C. APC/C has a ubiquitin ligase activity, which mediates proteolysis of its substrate proteins, securin and cyclin B1, at the mitotic period called the metaphase-to-anaphase (M/ A) transition (19). Proteolysis of securin induces activation of separase whose protease activity cleaves cohesin connecting sister chromatids. Proteolysis of cyclin B1 down regulates its associated cyclin-dependent kinase 1, or cdk1. In addition, separase that had been released from securin is known to bind to cyclin B1, and contributes also to inactivate cdk1 (9, 23). The relative significance of this separase-mediated inhibition of cdk1 remains to be investigated, however. Inactivation of cdk1 will give rise to dephosphorylation of cdk1 substrates at anaphase. We yet know little about what those cdk1 substrates are and what the effects of their dephosphorylation might be (22). The release of sister chromatid cohesion and subsequent separation of sister chromatids must occur coordinately to ensure fail-safe chromosome segregation (12). Degradation kinetics for securin and cyclin B1 determines the timepoints when their protein levels drop below the thresholds to commence anaphase events and is proposed to be under a robust system (13). Live cell imaging analyses for flu-