Mercury is a prominent environmental contaminant that causes endocrine disorder to human and other organisms. But little is known about the response of the thyroid functions and hypothalamic–pituitary–thyroid (HPT) axis to mercury in teleosts and the few studies that are available have not yielded consistent results. In this study, expression profiles of corticotropin-releasing hormone (crh), thyroid stimulating hormone beta (tshβ), solute carrier family 5 (sodium iodide symporter) member 5 (slc5a5), thyroglobulin (tg), thyroid hormone receptor alpha (trα) and thyroid hormone receptor beta (trβ) genes were determined in whole-body of Chinese rare minnow (Gobiocypris rarus) larvae after exposure to different levels of Hg2+ (0, 0.1 and 0.3mg/l) for 4 days, as well as the thyroid hormones (THs) levels. Moreover, the 96-h lethal concentration of Hg2+ on rare minnow larvae was determined as 0.32mg/l. The results showed that crh, tg, trα and trβ mRNA levels were significantly up-regulated in the larvae, but the gene expression of tshβ and slc5a5 was not significantly changed in our study. Besides, the THs levels increased in the whole-body of fish, especially the thyroxine (T4) level. The above results indicated that Hg2+ could alter some genes expression in the HPT axis which could be used as the potential biomarkers for evaluating the environmental Hg2+-induced stress in fish.