The role of lamprey epithelium tight junctions (TJs) in the regulation of salt and water balance is poorly understood. This study reported on claudin (Cldn) TJ protein transcripts of pre‐metamorphic larval and post‐metamorphic juvenile sea lamprey (Petromyzon marinus) and the transcriptional response of genes encoding Cldns to changed environmental ion levels. Transcripts encoding Cldn‐3b, ‐4, ‐5, ‐10, ‐14, ‐18 and ‐19 were identified, and mRNA expression profiles revealed the organ‐specific presence of cldn‐5 and ‐14, broad expression of cldn‐3b,
‐4, ‐10, ‐18 and ‐19 and spatial differences in the mRNA abundance of cldn‐4, ‐3b and ‐14 along the ammocoete intestine. Expression profiles were qualitatively similar in ammocoetes and juvenile fishes. Transcript abundance of genes encoding Cldns in osmoregulatory organs (gill, kidney, intestine and skin) was subsequently investigated after exposure of ammocoetes to ion‐poor water (IPW) and juveniles to hyperosmotic conditions [60% sea water (SW)]. IPW‐acclimated ammocoetes increased mRNA abundance of nearly all cldns in the gill. Simultaneously, cldn‐10 abundance increased in the skin, whereas cldn‐4, ‐14 and ‐18 decreased in the kidney. Ammocoete cldn mRNA abundance in the intestine was altered in a region‐specific manner. In contrast, cldn transcript abundance was mostly downregulated in osmoregulatory organs of juvenile fish acclimated to SW – cldn‐3b, ‐10 and ‐19 in the gill; cldn‐3b, ‐4, ‐10 and ‐19 in the skin; cldn‐3b in the kidney; and cldn‐3b and ‐14 in the intestine. Data support the idea that Cldn TJ proteins play an important role in the osmoregulatory physiology of pre‐ and post‐metamorphic sea lamprey and that Cldn participation can occur across organs, in an organ‐specific manner, as well as differ spatially within organs, which contributes to the regulation of salt and water balance in these fishes.