<div>Comparative genomics has become a central tool for evolutionary biology, and a better knowledge of understudied taxa represents the foundation for future work. In this study we characterized the transcriptome of male and female mature gonads in the European clam <i>Ruditapes decussatus</i>, compared to that in the Manila clam <i>Ruditapes philippinarum</i> providing, for the first time in bivalves, information about transcription dynamics and sequence evolution of sex-biased genes. In both the species we found a relatively low number of sex-biased genes (1,284, corresponding to 41.3 % of the orthologous genes between the two species), probably due to the absence of sexual dimorphism, and the transcriptional bias is maintained in only 33% of the orthologs. The dN/dS is generally low, indicating purifying selection, with genes where the female-biased transcription is maintained between the two species showing a significantly higher dN/dS. Genes involved in embryo development, cell proliferation, and maintenance of genome stability show a faster sequence evolution. Finally, we report a lack of clear correlation between transcription level and evolutionary rate in these species, in contrast with studies that reported a negative correlation. We discuss such discrepancy and call into question some methodological approaches and rationales generally used in this type of comparative studies.<br></div
