Here we present the first annotated de novo transcriptome assembly for a mesophotic sample of Agaricia lamarcki. Given the affordability of next generation sequencing, much more effort has been given to developing genomes and well-resolved transcriptomes for corals (Shinzato et al. 2014 Ortiz-González et al. 2016 Mansour et al. 2016 Anderson et al. 2016 Kenkel and Bay 2017). The ability to create annotated transcriptomes allows for insight into coral evolution and stress-response physiology (Kenkel et al. 2013 Bhattacharya et al. 2016 Lin et al. 2017). In addition, symbiont zonation is common among Caribbean corals and by sequencing its transcriptome, Agaricia lamarcki can be compared to other species which display depth-differentiated Symbiodinium (Bongaerts et al. 2013 2015). Few if any transcriptomes have been published from mesophotic habitats, thus the transcriptome reported within represents a novel resource for inferring coral gene functioning at depth. Understanding the genetic links between the holobiont and photosymbionts are paramount objectives for coral ecologists since anthropogenic influences such as global warming are likely to continue and worsen with time (Smith et al. 2015).