In order to investigate the relationship between estrogen receptor genes and growth differences in sexes and ploidy of fish, loach（Misgurnus anguillicaudatus）with females growing faster than males and tetraploids growing faster than diploids were selected as the research object in this study. We firstly cloned the cDNA sequences of three estrogen receptor genes of loach, including ER (1821 bp), ERβ1 (1008 bp) and ERβ2 (1197 bp). Amino acid sequence alignment revealed that loach ER genes have higher homology with corresponding subtypes of carps. Quantitative RT-PCR was used to detect the expression of ER genes in five growth stages of diploid loach as well as diploid and tetraploid adults. The results showed that three genes were differentially expressed in brain, muscle, liver, and gonadal tissues of male and female individuals before and after sexual maturity. Among them, the expression of ERα in brain, muscle and gonad tissues of male individuals was significantly higher than that of females (P<0.05), and the expression in female liver tissues was generally higher than that in males (P<0.05). The expression levels of ERβ1 and ERβ2 in testis tissue were always in high level. Comparison results between different ploidy showed that the expression of three ER genes in the diploid brain tissue were significantly higher than that of the tetraploids, and the expression levels of males were higher than females, with the expression of ERα being the most significant. The results of this study indicated that regardless of the difference between ploidy and sex growth, ERα appears to have relatively high expression in the brain tissue of slower growing (diploid, male) individuals. Therefore, we speculate that the ERα gene in brain tissues might have a certain inhibitory effect on the growth rate of individual fish.