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The Florida manatee (Trichechus manatus latirostris) has limited diversity in the immunoglobulin heavy chain. We therefore investigated the antigen receptor loci of the other arm of the adaptive immune system: the T cell receptor. Manatees are the first species from Afrotheria, a basal eutherian superorder, to have an in-depth characterization of all T cell receptor loci. By annotating the genome and expressed transcripts, we found that each chain has distinct features that correlates to their individual functions. The genomic organization also plays a role in modulating sequence conservation between species. There were extensive V subgroup synteny blocks in the TRA and TRB loci between T. m. latirostris and human. Increased genomic locus complexity correlated to increased locus synteny. We also identified evidence for a VHD pseudogene for the first time in a eutherian mammal. These findings emphasize the value of including species within this basal eutherian radiation in comparative studies.This is the first characterization of the TR loci within the Superorder Afrotheria.TR segmental diversity is comparable to other species despite low IgH diversity.T. m. latirostris TRD maintains CDR3 length despite having only one TRDD segment.There is V subgroup synteny between human and T. m. latirostris TRA and TRB loci.The first pseudogene VHD segment has been identified in a eutherian mammal.