Marine bivalves are commonly exposed to variable environmental conditions, among which temperature is a key factor that can affect many physiological processes of these ectotherms.To better understand molecular mechanisms underlying the physiological changes in response to thermal stress,we measured global transcriptional responses of scallop Chlamys farreri to acute (3h, 6h and 1d) and chronic (3d, 7d and 14 d) heat stress using the EcoP15I-tagged digital gene expression (EDGE) method. This study provides the first transcriptome-wide insights into molecular mechanisms underlying the physiological changes of scallops in response to thermal stress.