As nouns the difference between cilium and axoneme

is that cilium is a hairlike organelle projecting from a eukaryotic cell (such as a unicellular organism or one cell of a multicelled organism). These structures serve either for locomotion by moving or as sensors while axoneme is a bundle of nine microtubules forming the internal scaffolding of a cilium, with two extra central microtubules connecting the others if the cilium is motile.