To clarify the role of Wdr92, and R2TP, in motile cilium formation, we explored its function in Drosophila. We show that Drosophila Wdr92 is a cytoplasmic protein exclusively expressed in motile ciliated cells and is required exclusively for ciliary/flagellar motility. The major effect of its mutation is loss of dynein arms from the axonemes of sensory neuron cilia and sperm flagella. We confirm that Drosophila Wdr92 interacts with R2TP and that R2TP depletion also impairs dynein arm formation. We provide proteomic evidence that Wdr92 is associated especially with heavy chain assembly and propose that it acts as a specificity factor to bring axonemal dynein clients to the R2TP/HSP90 complex. Thus, Wdr92 is a new dynein assembly factor and it strongly reinforces the critical role of HSP90 and co-chaperones in dynein assembly.