The eukaryotic flagellum is a prominent organelle with conserved structure and diverse functions. Here we present a proteomic study of the flagella and pellicle of Euglena gracilis, a photosynthetic and highly adaptable protist, which employs its flagella for both locomotion and environmental sensing. The biochemically distinct flagella of this euglenozoan yields 1,684 protein groups, which challenges previous estimates on the protein composition of motile flagella across the eukaryotes.