Post-translational modifications of proteins change dramatically and dynamically protein structures and functions. Tubulin, which forms microtubules, undergoes highly unique post-translational modifications, polyglutamylation and polyglycylation. These modifications, in particular, accumulate in the axoneme of cilia or flagella. Recently, we and others have identified enzymes that perform or reverse those modifications. The discovery of enzymes enables to investigate the physiological roles of the modifications by means of model organisms with knockout or knockdown techniques. We here review recent knowledge, focusing on our own findings, about the roles of polyglutamylation and polyglycylation in ciliary or flagellar structure and motility.