Euglenophyta is a representative phylum of green-lineage secondary endosymbiotic eukaryotes. These organisms have evolved far-red light-harvesting complexes (LHCs) composed of diadinoxanthin and chlorophyll a/b, which are now classified as the LHCE family. Here we report a 2.35-Å cryo-electron microscopy structure of photosystem I (PSI) supercomplex from Euglena gracilis, with all subunits and their paralogs assigned. This structure reveals a minimal PSI core associated with twelve LHCE and four LHCII subunits. Most LHCE subunits are organized into dimers through a helix C–to–helix C interaction. Two dimers, together with a monomeric LhcE8, assemble into a (2 + 2 + 1)-type LHCE pentamer. The red-shifted pairs in the two LhcE6 subunits likely contribute to far-red absorption. The LHCII subunits form a distinct heterodimer and associate with the PsaF side. Overall, these results provide a structural basis for understanding energy transfer and dissipation, antenna subunit assembly, and far-red light-harvesting strategies in green-lineage secondary endosymbiotic organisms.