The thermal phenotype of an organism (heat and cold tolerance, thermal range, and thermal plasticity) is an essential feature of how the organism performs across thermal environments and in response to thermal stress. Porcelain crabs are of interest in addressing questions of thermal phenotype because of their high species diversity and the large variation in thermal phenotype among species, as well as the biogeographic patterning of these crabs along environmental stress gradients. We are studying the cellular bases of thermal phenotype and physiological responses to environmental stress using a functional genomics cDNA microarray approach. To do this, we have isolated total RNA from a range of tissues from I species of porcelain crab (Petrolisthes cinctipes) exposed to a suite of thermal conditions, and have used this RNA to construct a 13 824-clone EST library. Here, we describe construction, EST sequencing, assembly and clustering, and results of BLASTx homology search for our initial 13 824-clone library. From 12 060 usable ESTs, 6717 consensus sequences were identified, and roughly 50% of these have homology to known proteins. At present, an additional 50 000-75 000-clone library of P. cinctipes ESTs is being generated, with the aim of developing a library with near-complete coverage of the transcriptome. The libraries and sequence information that will be generated as a result of this project should be of value for crustacean biologists working across a broad range of scientific disciplines (for example, physiology, developmental biology, biological rhythms, ecology, fisheries biology), as well as in studies of molecular evolution and phylogeography.