Recognition of the mRNA 5′ end is a critical step needed for translation initiation. This step is performed by the cap binding protein eIF4E, which joins the larger eIF4G subunit to form the eIF4F complex. Trypanosomatids have a minimum of fve diferent eIF4F-like complexes formed through specifc but not well-defned interactions between four diferent eIF4E and fve eIF4G homologues. The EIF4E6/EIF4G5 complex has been linked with the stage-specifc translation of mRNAs encoding the major Trypanosoma brucei virulence factors. Here, to better defne the molecular basis for the TbEIF4E6/TbEIF4G5 interaction, we describe the identifcation of the peptide interacting with TbEIF4E6 in the region comprising residues 79–166 of TbEIF4G5. The TbEIF4E6-TbEIF4G5_79-116 complex reconstituted with recombinant proteins is highly stable even in the absence of cap-4. The crystal structure of the complex was subsequently solved, revealing extensive interacting surfaces. Comparative analyses highlight the conservation of the overall structural arrangement of diferent eIF4E/eIF4G complexes. However, highly diferent interacting surfaces are formed with distinct binding contacts occurring both in the canonical and noncanonical elements within eIF4G and the respective eIF4E counterpart. These specifc pairs of complementary interacting surfaces are likely responsible for the selective association needed for the formation of distinct eIF4F complexes in trypanosomatids.