Based on the existence of genetic resources and phenotypic differentiation in Crassostrea gigas and Crassostrea angulata populations, the present study aims to compare reproductive related traits especially at the transcriptomic level of C. gigas, C. angulata and their hybrids. We analyzed the whole gonad transcriptome of progenies of wild Pacific and Portuguese oysters and their hybrids under a common garden experiment using the Illumina’s sequencing technology. The obtained sequences and the means of expression patterns were analysed to 1) estimate whether the gene expression changes are in some fashion ‘directed’ by the dictates of hybrid vigour, maternal effects, or other factors (stochastic changes being integrated here), 2) identify some differentially expressed genes of interest that may correlated with reproductive peculiarities of each taxon, and 3) call single nucleotide polymorphisms (SNPs), separate synonymous versus non-synonymous variants, and estimate the level of genetic polymorphism for each taxa .