Claudins are four-transmembrane proteins acting to collectively regulate paracellular movement of water and ions across cellular tight junctions in vertebrate tissues. Despite the prominence of zebrafish (Danio rerio) as a developmental model and the existence of an annotated genome, the diversity and evolutionary history of these claudins, with respect to other vertebrate groups, is poorly described. In this study, we identify 54 zebrafish claudins, including 24 that were previously unreported, and infer homology of the encoded polypeptide sequences with other vertebrate claudin groups using Bayesian phylogenetic analysis. In this analysis, 197 vertebrate claudin and claudin-like proteins were classified into discrete ‘superclades’ of related proteins. Based on these groupings, an interim reclassification is proposed, which will resolve ambiguity in the present nomenclature of several vertebrate models. Fifty-two of the 54 identified claudins were detected in cDNA preparations from whole, adult zebrafish, and 43 exhibited distinct tissue expression profiles. Despite prolific expansion of the claudin gene family in teleost genomes, these claudins can still be broadly separated into two functional groups: (1) “classic” claudins that characteristically contain an equal number of opposing, charged residues in the first extracellular loop (ECL1) and (2) “non-classic” claudins that typically have an ECL1 containing a variable number of charged residues. Functional analysis of these groups indicates that ‘classic’ claudins may act to reduce overall paracellular permeability to water and dissolved ions, whereas ‘non-classic’ claudins may constitute pores that facilitate selective ion permeability.