Cilia show a remarkable structural conservation across eukaryotes. Nevertheless, there are still different types of configuration such as the 9+2 structure of motile cilia (a central pair of single microtubules surrounded by nine pairs of double microtubules) or the 9+0 structure of non‐motile cilia. Cilia are constructed by intraflagellar transport (IFT) whereby large protein complexes driven by kinesin and dynein motors deliver the necessary components to the ciliary tip for assembly. Recent data from Trypanosoma brucei revealed that the IFT trains are restricted to only some of the axonemal doublet microtubules. In article 2200031, Adeline Mallet and Philippe Bastin propose two hypotheses that help to explain this restriction and discuss how this opens possibilities for the evolution of cilia towards more complex or simpler configurations.