Cilia and flagella are central to many biological processes in a diverse range of organisms. The kinetoplastid protozoa are very appealing models for the study of flagellar function, particularly in the light of the availability of extensive trypanosomatid genome information. In addition to the highly conserved 9 ؉ 2 axoneme, the kinetoplastid flagellum contains a characteristic paraflagellar rod structure (PFR). The PFR is necessary for full motility and provides support for metabolic regulators that may influence flagellar beating. However, there is an intriguing puzzle: one clade of endosymbiont-containing kinetoplastids apparently lack a PFR yet are as motile as species that possess a PFR and are able to attach to the invertebrate host epithelia. We investigated how these organisms are able to locomote despite the apparent lack of PFR. Here we have identified a PFR1 gene in the endosymbiont-bearing trypanosome Crithidia deanei. This gene is expressed in C. deanei and is able to partially complement a pfr1 null mutation in Leishmania mexicana cells, demonstrating that the encoded protein is functional. Careful reexamination of C. deanei flagellar ultrastructure revealed a greatly reduced PFR missed by many previous analyses. This affirms the PFR as a canonical organelle of kinetoplastids. Moreover, although PFR proteins have been conserved in evolution, primary sequence differences contribute to particular PFR morphotypes characteristic of different kinetoplastid species.Cilia and flagella are central to many biological processes in a diverse range of organisms. In the order Kinetoplastida-the group of flagellates that include trypanosomatid parasites and bodonids-the flagellum is the classical organelle of motility (42). In parasitic species, the kinetoplastid flagellum has also evolved to be an organelle of attachment to the invertebrate vector, playing a critical role in parasite transmission to the vertebrate host (42). Moreover, recent work shows that the kinetoplastid flagellum is also involved in cell division; positioning of the new flagellum, one of the earliest event in cell duplication, defines the axis of polarity in the dividing cell and the position of the internal organelles (31). Finally, flagellar wave reversal in a Ca 2ϩ -dependent manner as an avoidance response has been studied in trypanosomatids (39), suggesting that the flagellum in these species may also be a specialized sensory organelle.The main component of both cilia and flagella is the axoneme. This microtubule-based organelle was most probably present in the ancestor of all modern eukaryotes and is highly conserved in several deeply diverged lines. In many organisms, the axoneme is augmented by extra-axonemal structures-for example, the fibrous sheath in mammalian spermatozoa and the R-fiber of dinoflagellates. In the Kinetoplastida, a characteristic structure known as the paraflagellar rod (PFR) runs alongside the axoneme to form the flagellum. This PFR is an elegant and stable lattice-like arrangement of protein filaments which ...