The high coefficient of determination obtained confirmed the high reliability of the microarray approach. This value was even shifted up when genes displaying low expression, and therefore less reliable Ct values in the correlation were excluded. Gonad samples were collected from Pacific oysters originating from 3 different sampling sites, at the four stages of the yearly reproductive cycle of oysters. This sampling method was undertaken in order to compensate for a possible bias in Atropine sulfate transcriptome analysis due to singularity of a single population within a precise environmental context. The results were mainly obtained from studying transcriptomic profiles from site 1 individuals, and show that the transcriptome of samples collected from different geographical locations are not significantly different regarding gametogenesis. Thus, we compared the transcriptomes of gonads from site 1 and site 2 using both microarray and real time qPCR analyses. The high correlation between geographical locations confirmed that the expression profiles observed are real features of gametogenesis in oysters without significant influence of the sampling site. Our analysis provided lists of genes Catharanthine sulfate expressed in male and female gonads, genes that increase in expression along the gametogenetic cycle, genes expressed in the flagella structure of spermatozoids, genes expressed in oocytes and genes expressed by female somatic cells. Most importantly, cross-referencing these lists of genes allowed us to identify potential markers of early sex differentiation in C. gigas oyster, a singular alternative hermaphrodite mollusk. We also provided new highly valuable information on genes specifically expressed by mature spermatozoids and mature oocytes. We initially hoped to use PCA to discriminate between male and female stage 0 oysters and to identify genes involved in early sex differentiation. However, no difference was observed between the eight stage 0 gonads analyzed. Therefore, the future sexual development of these gonads could not be predicted from this PCA analysis. Principal component analysis revealed that differences between males and females increased overtime, from stage 1 gonads to stage 3 gonads, suggesting that sex differentiation takes place sometime before. Interestingly, some of the studied stage 0 gonads were found to express male specific or female specific genes, suggesting that sex differentiation already took place within these individuals although it was not possible to sex them using histology. We did not observe mitosis and cell proliferation within these individuals by histological methods. However, we performed cytology by observing a single transverse section of the gonad collected in the middle of the organ. Heterogeneity in the development of germ cells at different levels of the gonad has been observed and this may explain that some sex specific genes are found expressed when gene expression is measured on the whole gonad. Thus, the individuals presumed to be at stage 0 according to histological characterization, may biologically correspond to early stage 1 individuals. Few differences were observed between the transcriptomic profiles of undifferentiated stage 0 and sexed stage 1 individuals. Differences seem to fit with germ cell proliferation and the onset of meiosis in stage 1. The mitosis/ meiosis and sperm/oocyte decision may take place during the same time frame in the oyster gonad. In C. elegans, fbf and gld-3 genes control both the decision to leave the mitotic cell cycle and enter meiosis and to achieve the switch from spermatogenesis to oogenesis.