Guanylin (GN) stimulates Cl− secretion into the intestinal lumen of seawater-acclimated eels, but the molecular mechanisms of transepithelial Cl− transport are still unknown. In Ussing chamber experiments, we confirmed that mucosal application of eel GN reversed intestinal serosa-negative potential difference, indicating Cl− secretion. Serosal application of DNDS or mucosal application of DPC inhibited the GN effect, but serosal application of bumetanide had no effect. Removal of HCO3– from the serosal fluid also inhibited the GN effect. In intestinal sac experiments, mucosal GN stimulated luminal secretion of both Cl− and Na+, which was blocked by serosal DNDS. These results suggest that Cl− is taken up at the serosal side by DNDS-sensitive anion exchanger (AE) coupled with Na+–HCO3– cotransporter (NBC) but not by Na+-K+-2Cl− cotransporter 1 (NKCC1), and Cl− is secreted by unknown DPC-sensitive Cl− channel (ClC) at the mucosal side. The transcriptomic analysis combined with qPCR showed low expression of NKCC1 gene and no upregulation of the gene after seawater transfer, while high expression of ClC2 gene and upregulation after seawater transfer. In addition, SO42− transporters (apical Slc26a3/6 and basolateral Slc26a1) are also candidates for transcellular Cl− secretion in exchange of luminal SO42. Na+ secretion could occur through a paracellular route, as Na+-leaky claudin15 was highly expressed and upregulated after seawater transfer. High local Na+ concentration in the lateral interspace produced by Na+/K+-ATPase (NKA) coupled with K+ channels (Kir5.1b) seems to facilitate the paracellular transport. In situ hybridization confirmed the expression of the candidate genes in the epithelial enterocytes. Together with our previous results, we suggest that GN stimulates basolateral NBCela/AE2 and apical ClC2 to increase transcellular Cl− secretion in seawater eel intestine, which differs from the involvement of apical CFTR and basolateral NKCC1 as suggested in mammals and other teleosts.