The estuarine tapertail anchovy (Coilia nasus) is a widely-distributed and commercially-important aquaculture species. In this study, two prostaglandin E synthase 2 (PTGES2) orthologs were identified. The full length ortholog PTGES2a was 1,575 bp and contained a 1,167-bp Open Reading Frame that encoded a protein of 388 amino acids. The 5′ and 3′ untranslated regions were 269 bp and 139 bp, respectively. The full length ortholog PTGES2b was 1,457 bp and contained a 729-bp ORF that encoded a protein of 242 amino acids. The 5′ and 3′ untranslated regions were 402 bp and 326 bp, respectively. One polyadenylation signal (AATAAA) was present 14 nucleotides upstream of the poly(A) tail in both the PTGES2aand thePTGES2bgene. The full-length genomic DNA sequence of PTGES2a is 3,222 bp long, and composed of seven exons and six introns. The full-length genomic DNA sequence of PTGES2b is 1,908 bp long, and composed of six exons and five introns. PTGES2a was strongly expressed in the gills and liver while PTGES2b was strongly expressed in the gills and testis. Expression of both PTGES2a and PTGES2b decreased from stage III to stage V and PTGES2a was significantly more highly expressed than PTGES2b. In the spawning process, the expression of PTGES2a did not significantly change, remaining at a low level. In contrast, PTGES2b expression significantly increased during spawning. These results provide basic knowledge of the new PTGES2s of C. nasus.