Calcitonin gene-related peptide (CGRP) is a 37-amino acid neuropeptide that has been identified in teleosts and mammals. Calcitonin receptor-like receptor (CLR) forms the CGRP receptor. In teleost fish, CGRP plays a role in vasodilation and is associated with osmotic regulation. However, the embryonic function of CGRP remains unclear. Therefore, we have investigated CGRP function related to early development in the flounder, Paralichthys olivaceus. We first identified two CLRs from the flounder genome database. According to molecular phylogenetic analysis, two CLRs are classified in the group formed by teleost CLR1 and 2. They represented high amino acid sequence identity among mefugu CLR1-3 and human CLR. We also identified another CLR/CTR candidate from the flounder genome. Molecular phylogenetic analysis revealed that this gene was located at the clade formed by vertebrate CTRs that are CLR paralogs. The deduced protein of the gene also had four hormone-binding domains, which are the typical feature of teleost CTR, and was completely different from the CLR of teleosts, including flounder CLRs. These data strongly suggest that flounder possess two putative CGRP receptors. Finally, we performed the expression analysis of flounder CGRP and two CLRs in the flounder embryo. Both expressions of CGRP mRNA and two CLR mRNAs were detected from 96 hours post fertilization (hpf). These results demonstrate that CGRP has some functions at 96 hpf. At that stage, embryos have already hatched and the circulatory system functions, whereas digestive organs still continue to develop. Taken together, these findings suggest that the CGRP peptide may play a role in the circulatory system, as in adult fish, or it may be associated with the development of the digestive tract.