The molecular expression profiles of zebrafish ep2a and ep4b have not been defined to-date. Phylogenetic trees of EP2a and EP4b in zebrafish and other species revealed that human EP4 and zebrafish EP4b were more closely related than EP2a. Zebrafish EP2a is a 281 amino acid protein with high identity to that of human (43%), mouse (44%), rat (43%), dog (44%), cattle (41%), and chicken (41%). Zebrafish EP4b encoded a precursor of 497 amino acids with high amino acid identity to that of mammals, including human (57%), mouse (54%), rat (55%), dog (55%), cattle (56%), and chicken (54%). Whole-mount in situ hybridization revealed that ep2a was robustly expressed in the anterior four somites at the 10-somites stages, but was absent in the somites at 19 hpf. It was observed again in the pronephric duct at 24 hpf, in the intermediate cell mass located in the trunk, and in the rostral blood island at 30 hpf. Ep2a was also expressed in the notochord at 48 hpf. During somitogenesis, ep4b was highly expressed in the eyes, somites, and the trunk neural crest. From 30 to 48 hpf, ep4b could be detected in the posterior cardinal vein and the neighboring ICM. From these data, we conclude that ep2a and ep4b are conserved in vertebrates and that the presence of ep2a and ep4b transcripts during developmental stages infers their role during early zebrafish larval development. In addition, the variable expression of the two receptor isoforms was strongly suggestive of divergent roles of molecular regulation.