Copepods are fundamental components of zooplankton and aquatic pelagic food webs, but reports on molecular responses linked to reproductive success under in situ conditions are still scarce. We present a de novo transcriptome and differential expression (DE) analysis in wild Temora stylifera females collected in the Gulf of Naples, Mediterranean Sea, where this copepod represents one of the dominant species. RNA-Seq and DE analysis were performed from females collected on consecutive sampling weeks (May 23rd and 30th 2017), because opposite naupliar survival rates were observed (25% on May 23 rd , test and 93% on May 30 th , control). We aimed at detecting key genes that may have influenced in situ copepod reproductive potential and whose expression may have been affected by phytoplankton-derived oxylipins, lipoxygenase-derived products impacting copepod naupliar survival.