Leptin has been well-established as a canonical anorexic peptide hormone in mammals, though much of its function in fish remains obscure. In this study, the cDNAs of two leptin isoforms (leptin-A and leptin-B) were cloned from the liver of a small cyprinid fish, Tanichthys albonubes. The two T. albonubes leptins, sharing low primary amino acid sequence homology with their mammalian counterparts, and between themselves, are highly conserved in three-dimensional protein structures and gene structures. Liver is a major source of leptin mRNA in T. albonubes with leptin-A being the dominant form. The expression of hepatic leptin-A but not leptin-B mRNA in female fish is significantly higher than in male fish. Transcriptional hepatic levels of leptin-A and leptin-B in both male and female fish were demonstrated to increase after long-term fasting (10-25days) but decline upon re-feeding (3days). Strikingly, estrogen (E2) administration induced only leptin-A but not leptin-B hepatic mRNA expression in both male and female fish. Our study here provides the first evidence for differential regulation of two leptins in fish, and sheds new light on the possible origin of leptin in lower vertebrates.