Therefore, this study was designed to provide a better to establish lists of genes of interest specific to each reproductive stage and sex. We employed a custom oligonucleotide microarray containing 31,918 ESTs Gomisin-D described and validated in Dheilly et al.. Our study identifies novel sex specific molecular markers and genes differentially expressed over the different stages of the gametogenesis cycle of males and females. Five hundred and eleven genes decreased in expression along the gametogenetic cycle. Numerous genes were previously identified as tissue-enriched in either the digestive gland, the mantle tissue, the visceral ganglion, hemocytes or the adductor muscle by Dheilly et al.. The method we employed did not exclude the possibility that genes that appear more expressed in early gonad developmental stages than in maturing gonads could be artifacts due to a dilution effect of genes expressed in somatic tissues, such as muscular fibers surrounding the gonadal tubules, when germ cells accumulate within the gonad area. In order to identify genes specifically expressed during early gametogenetic stages, we searched for genes significantly more expressed in immature gonads than in somatic tissues and mature gonads. Thus we compared expression data in stage 0 oyster gonads with expression data from somatic tissues previously described in Dheilly et al. in order to differentiate germline specific genes and genes somatically expressed in our gonad samples. Oyster gonad is a mixed tissue including storage tissue, smooth muscle fibers and circulating hemocytes. In order to characterize the expression of genes involved in gametogenesis in oocytes or female somatic tissue, we studied the transcriptome of oocytes collected by stripping 7 mature females and compared them to the transcriptome of the 10 stage 3 female gonad samples. Among the 2,482 genes differentially expressed in both male and female gametogenesis, 434 were significantly differentially expressed between female gonad tissue and stripped oocytes. Genes for which more transcripts were found in whole stage 3 gonads are predicted to be expressed by female somatic tissues. When more transcripts were found in stripped mature oocytes, the genes are predicted to be expressed by female germ cells. Predicted localization of gene expression is provided in file S3. Recent expression profiling studies using microarrays have provided great insight into the molecular mechanisms governing various complex physiological traits. Among those, the unprecedented amount of Butenafine hydrochloride information collected on gametogenesis, mitosis or meiosis of different eukaryotes such as yeast or nematode had a great impact on our understanding of sexual reproduction. Microarrays have also been employed successfully to better understand the cellular and molecular events of the development of reproductive tissues and of embryogenesis of cattle, mouse, rat and fish. Here, we proposed to unravel some molecular mechanisms involved in sex differentiation and gametogenesis of a peculiar alternative hermaphrodite invertebrate, the Pacific oyster Crassostrea gigas. We used an oligonucleotide microarray composed of 31,918 ESTs to characterize the transcriptome of oyster gonads at different developmental stages. The microarray employed in this study had previously been used to describe the transcriptome of various tissues of C. gigas and the results were validated by showing a significant correlation of gene expression obtained by real time qPCR and microarrays.