Sabellaria alveolata is a reef-building polychaete that inhabits the rocky intertidal zone of Europe. As an intertidal species, S. alveolata has likely developed adaptations to cope with wide temperature fluctuations, being exposed to both air and sea surface temperatures that vary daily and seasonally across its range. To investigate the ability of the honeycomb worm to respond to temperature stress, individuals from five geographically distinct populations spanning the species' distribution (Scotland, English Channel coast of France, southern Atlantic coast of France, Portugal and Morocco) were collected and maintained under controlled common garden conditions. After one month of acclimation at 15C (T0), temperature was increased by 1C per day until reaching 20C (T1), followed by a four-week acclimation period (T2). A second temperature challenge was then conducted by increasing the temperature by 1C per day to 25C (T3), followed by another four-week acclimation period (T4). Whole organisms were collected at experimental ssampling time point (T0-T4) from each population and placed in Trizol (Life Technologies), followed by flash freezing in liquid nitrogen. RNA was extracted with chloroform and percipitated in ethanol. RNA quality was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies,), and was quantified using the Quant-IT RiboGreen RNA Assay Kit (Life Technologies). Library preparation and sequencing were performed at Christian-Albrechts-Universitat, Kiel, Germany, using an Illumina HiSeq2000 platform in October 2014. Paired-end sequencing (2 100 bp) was conducted to generate high-quality transcriptomic data.