Eukaryotic motile cilia/flagella are conserved organelles important for cell propulsion and fluid flow, typically built around a "9+2" axoneme of nine doublet microtubules (DMTs) encircling a central pair of singlet microtubules. The DMT lumen is lined with an interconnected network of microtubule inner proteins (MIPs), some conserved and others lineage-specific. MIPs augment the tubulin lattice of the DMT, directly impacting stability, fine structure, and motility, thus providing an important source of lineage-specific adaptations.Trypanosoma bruceiis a flagellated eukaryotic pathogen with distinctive motility that is critical for pathogen transmission and pathogenesis. Prior studies revealed lineage-specificT. bruceiMIPs, but their identities are unknown. To identifyT. bruceiMIPs, we examined flagellum structure and composition following knockdown of FAP106, a conserved MIP at the inner junction (IJ) connecting A- and B-microtubules of the DMT. FAP106 knockdown resulted in short flagella and defective parasite motility, supporting a role for MIPs inT. bruceiflagellum stability and motility. Cryogenic electron tomography (cryoET) and quantitative proteomics identified several conserved MIPs and lineage-specific MIP structures and MIP candidate proteins (MCs) that depend on FAP106 for stable assembly. We further demonstrate by knockdown and fitting AlphaFold models to cryoET maps that one of these, MC8, is a newly identified lineage-specific MIP required for normal parasite motility. This work provides an important advance toward elucidating the order of assembly of MIPs at the cilium inner junction and identifies trypanosome proteins specific to these deadly pathogens that represent targets to consider for therapeutic intervention.