Sexual differentiation and ovotestis development are closely associated with cortisol levels, the principal indicator of stress, via the glucocorticoid receptor (GR) in teleosts. Thus, GR is regarded as a mediator to expound the relationship between social stress and gonad development. In the present study, two gr genes (gr1 and gr2) were cloned and analyzed from a protandrous hermaphroditic teleost, the yellowtail clownfish (Amphiprion clarkii). GR1 was found to display a conserved nine-amino-acid insert, WRARQNTDG, between two zinc finger domains. The phylogenetic tree of GR showed that yellowtail clownfish GR1 and GR2 are clustered to teleost GR1 and teleost GR2 separately, and differ from tetrapod GR. The result of real-time PCR revealed that high-level gr1 was mainly distributed in the cerebellum, hypothalamus and heart. The gr2 gene was abundant in the pituitary and liver of females and nonbreeders, while gr2 was mainly detected in the medulla oblongata and middle kidney of males. Moreover, GRs can be expressed in cultured eukaryotic cells and functionally interact with dexamethasone (exogenous glucocorticoid), thereby triggering downstream signaling pathways of different potentials. GR1 and GR2 can be activated by 10 nM dexamethasone treatment in HEK-293T cells. Notably, real-time PCR analysis among three social status groups demonstrated that gr2 expression was the highest in the hypothalamus of nonbreeders, but gr1 was no difference. We speculate that social stress would increase the expression of gr2 gene expression in the hypothalamus to inhibit sexual development. These data provide evidence of social stress involving reproductive regulation, which may help to elucidate the underlying mechanism of sex differentiation and change.