We isolated four variants of ER α mRNA, two each from the brain and gonad of the Xenopus embryo (brain, bER α 1 and bER α 2; gonad, gER α 1 and gER α 2). The N-terminal-domain of ER α differed between the brain and gonad. While the C-terminal region downstream of the DNA-binding domain of ER α differed between ER α 1 and ER α 2 in both the brain and gonad, each of ER α 1 and ER α 2 contained the same sequence sets (bER α 1 and gER α 1; bER α 2 and gER α 2) between the brain and gonad. Both bER α 1 and gER α 1 contained the same full-length, C-terminal estrogen receptor, whereas the C terminus of bER α 2 and gER α 2 lacked half of the DNA-binding, ligand-binding, and transcriptional activation domain. Although gER α was mainly expressed in the gonad, both bER α and gER α were expressed in the brain of the Xenopus embryo at stage 50. These isoforms might be transcribed by alterative splicing of a single gene. Two gonad ER β s differing in the length of the N-terminal sequence were isolated from the Xenopus gonad. While ER β was expressed in the gonad, it was not expressed in the brain of the Xenopus embryo at stage 50.