The rise of seawater temperature is projected to affect the health, growth, survival and distribution of marine mollusks. The ark shell, Scapharca subcrenata, are susceptible to high temperature in summer, which may cause vibrio diseases by reducing the immune function and then lead to mass mortality. Herein, we conducted the transcriptome analysis of haemocytes in ark shell under thermal stress and control conditions, to reveal the molecular mechanism against acute heat stress.