Proper activation of checkpoint during mitotic stress is an important mechanism to prevent genomic instability. Chfr (Check point protein with FHA (Forkhead-associated domain) and RING domains) is a ubiquitin-protein isopeptide ligase (E3) that is important for the control of an early mitotic checkpoint, which delays entry into metaphase in response to mitotic stress. Because several lines of evidence indicate that Chfr is a potential tumor suppressor, it is critically important for us to identify Chfr substrates and understand how Chfr may regulate these substrates, control mitotic transitions, and thus, act as a tumor suppressor in vivo. Here, we report the discovery of a new Chfr-associated protein Kif22, a chromokinesin that binds to both DNA and microtubules. We demonstrated that Kif22 is a novel substrate of Chfr. We showed that Chfr-mediated Kif22 down-regulation is critical for the maintenance of chromosome stability. Collectively, our results reveal a new substrate of Chfr that plays a role in the maintenance of genome integrity.