Axonemal dynein motors are large multisubunit complexes that drive ciliary movement. Cytoplasmic assembly of these motor complexes involves several co-chaperones, some of which are related to the R2TP co-chaperone complex. The different roles of these co-chaperones is not completely known. Two such dynein assembly factors (DNAAFs) that are thought to function together in an R2TP-like complex are DNAAF4 (DYX1C1) and DNAAF6 (PIH1D3). Here we investigate the Drosophila homologues, CG14921/Dnaaf4 and CG5048/Dnaaf6. Surprisingly, Drosophila Dnaaf4 is truncated such it lacks a TPR domain, which is proposed to recruit HSP90 in human DNAAF4. Despite this, we provide evidence that Dnaaf4 and Dnaaf6 proteins can associate in an R2TP-like complex, and show functional conservation. Both are specifically expressed and required in the development of the two Drosophila cell types with motile cilia: mechanosensory chordotonal neurons and sperm. Flies that lack either gene are viable but with impaired chordotonal neuron function and lack motile sperm. We provide evidence that Dnaaf4 and Dnaaf6 are required for assembly of ODAs and a subset of IDAs.