Cilia are highly conserved organelles responsible for cell motility and sensing of extracellular signals. The core component of cilia is the ‘9+2′ axoneme, which comprises nine outer doublet microtubules and a central apparatus (CA) composed of two singlet microtubules with associated projections. The CA is essential for ciliary motility, and defects in it are associated with several human diseases, such as chronic respiratory infections and infertility. However, the protein composition and function of most CA projections remain unknown. Now, Daniela Nicastro and colleagues (Cai et al., 2021) use different approaches to characterise three CA candidate proteins in Chlamydomonas. First, they show that mutants lacking FAP246, FAP42 or FAP413 exhibit altered swimming pattern, suggesting that these proteins play a role in flagellar motility. Next, analysis of the axonemal proteome by mass spectrometry suggests the three proteins are part of the same complex. In addition, using cryo-electron tomography and subtomogram averaging to investigate the CA structure in these mutants, the authors show that these proteins localise at the C1b projection of the CA. Moreover, they demonstrate that the FAP246–FAP413–FAP42 complex is essential for the stable assembly and positioning of neighbouring structures in the C1b, C1f and C2b projections. Overall, this study thus advances our understanding of the ultrastructure of the ciliary CA by revealing the organisation of the C1b projection and its importance for flagellar motility.