Cytokinesis is the last step in the cell cycle, where daughter cells finally separate. It is precisely regulated in both time and space to ensure that each daughter cell receives an equal share of DNA and other cellular materials. Chemical biology approaches have been used very successfully to study the mechanism of cytokinesis. In this review, we discuss the use of small molecule probes to perturb cytokinesis, as well as the role naturally occurring small molecule metabolites such as lipids play during cytokinesis.