The cycle of ciliogenesis and ciliary disassembly is coordinated with cell division. In the unicellular alga Chlamydomonas, the two flagella are maintained at constant and equal length during interphase, and are reabsorbed prior to mitosis. We report that the NIMA-related kinase, Cnk2p, is an axonemal protein that affects flagellar length via effects on disassembly rate and also plays a role in the cellular assessment of size prior to committing to mitosis. This is the second NIMA-related kinase shown to affect ciliary function and cell cycle progression in Chlamydomonas. We speculate that members of the NIMA family have evolved nuanced roles to coordinate cilia/cell cycle regulation.