T cell receptor (TCR) chains are composed of two extracellular domains, the membrane-distal variable domain and the membrane-proximal constant domain. Data presented here show that the TCRA 'constant' (C) domain of damselfish exhibits considerable allelic polymorphisms that appear to be positively selected. Each of 32 damselfish TCRAC clones showed different patterns of atypical polymorphism in the constant region. Twenty-three of the 121 TCRalpha constant region amino acid residues show substitutions, clustered mainly in the loops between the beta strands. Coding regions of the TCRAC genes differ by up to 8% at the nucleotide level and 20% at the amino acid level. Southern hybridization, polymorphism segregation, and genomic cloning data suggest allelic polymorphism at two TCRAC genes, distinguished by a single amino acid. KA/KS ratios suggest that balancing selection is acting to maintain polymorphisms at the variable sites of one of these genes, but not the other, in a manner comparable to the peptide binding regions of MHC. Nonetheless, each TCRAC gene is spliced to variable and joining segments similar to those described in other species. These data suggest that our understanding of the function of the TCR constant domains of these vertebrates is incomplete.