Significance The distal end of the eukaryotic flagellum/cilium has critical functions, yet due to its small dimensions and association of tip structures with the axoneme is rather intractable to studying. We have developed biochemical approaches to identify a cohort of proteins specific for the flagellum tip structures. We sublocalized these proteins into individual structures. Using functional studies, we elucidated how the identified proteins contribute to the function of the flagella connector, the mobile membrane junction at the tip of the trypanosome flagellum.