A variety of strategies for sex determination mechanisms have been utilized in vertebrates. The Sox9 gene encodes a transcription factor that is critical for testis determination and chondrogenesis in vertebrates. We present here the polymorphisms of the Sox9a gene in population in the rice field eel, a fresh-water fish with naturally sex reversal characteristic from female via intersex into male during its life. Two alleles of the Sox9a2 were found in the population, which may potentially be associated with the dimorphic distribution of the male population of the rice field eel. J. Exp. Zool. (Mol. Dev. Evol.) 299B:36–40, 2003. © 2003 Wiley-Liss, Inc.