Mammalian CD45 is a transmembrane protein tyrosine phosphatase expressed by all nucleated cells of hematopoietic origin. In lymphocytes, CD45 is required for Ag-induced signal transduction due to its ability to positively regulate Src family members. The mechanisms by which CD45 function is regulated are unknown. Indeed, the interactions of CD45 extracellular domains are largely undefined. To gain insight into potentially important regions of the extracellular domain, we sought to identify conserved features from divergent species. cDNAs encoding the putative CD45 homologue from Heterodontus francisci (horned shark) were isolated. The cDNA sequence predicts a protein of 1200 amino acids that contains a 452-amino acid extracellular domain, a 22-amino acid transmembrane region, and a 703-amino acid cytoplasmic domain. Alignment searches revealed that the Heterodontus cytoplasmic domain sequence was most identical to mammalian CD45 and a transmembrane protein tyrosine phosphatase sequence identified from chickens, ChPTP lambda. A dendrogram with other transmembrane protein tyrosine phosphatase sequences suggest that the Heterodontus and chicken sequences represents CD45 orthologues for their respective species. Analysis of vertebrate CD45 extracellular domain sequences indicates the conservation of three structural regions: a region containing potential O-linked carbohydrate sites, a cysteine-containing region, and a region containing three fibronectin type III domains. For each vertebrate species, multiple isoforms are generated by alternative splicing of three exons that encode a portion of the region containing potential O-linked glycosylation sites. These studies provide evidence for a conservation in CD45 extracellular domain structure between divergent species and provide a basis for understanding CD45 extracellular domain interactions.