Through RNA sequencing, we investigated sex-specific differences in gene expression in brains and gonads of two teleost species belonging to Sparidae family, the common pandora Pagellus erythrinus and the red porgy Pagrus pagrus. Our aim was to capture the transcriptomic signature of different sexes in these protogynous hermaphrodite sparids and shed light into the molecular network contributing to either the female or the male phenotype in these organisms.