The central bearded dragon (Pogona vitticeps) has a ZZ male/ZW female sex chromosome system. The Z and W are tiny (microchromosomes), but they are easily distinguishable microscopically by the regions of repetitive sequence on the larger W. We searched the sex chromosome sequences for candidate sex determining genes, but could find no differences in coding genes between the Z and W. The most promising candidate gene was Nr5a1, which codes for steroidogenic factor SF1, a protein essential for mammalian sex determination. This gene has alleles on both the Z and W (Z-nr5a1 andW-nr5a1), which have the same genomic sequence, and are subject to recombination. Three isoforms were detected in Z-nr5a1 transcripts from gonads of adult ZZ males, two of which would translate into intact protein. However, the Z-nr5a1 and W-nr5a1 alleles of ZW females produced sixteen isoforms, most of which contained chain terminating sequences. This suggests that the W-borne allele produces transcripts that are differentially spliced and produce truncated polypeptides. Structures of these truncated polypeptides confirm that the DNA binding domain is intact, so that they could act as competitive inhibitors of the full length intact protein. We propose that an altered configuration of the W chromosomes affects the conformation of the primary transcript to generate inhibitory W-borne isoforms that suppress testis determination. Thus this GSD system may be controlled, not genetically but epigenetically, by the sex chromosomes.