Although hemocytes of bivalve molluscs play an important and central role in the internal defense, the exact mechanism of cell maturation events are quite less familiar. To further study the molecular regulatory mechanisms of hemocytes maturation, we applied quantitative transcriptomic analysis of two oyster hemocyte subpopulation. Granulocytes and hyalinocytes were sorted from the Pacific oyster Crassostrea gigas hemolymph in this study via flow cytometry on the basis of their cellular granularity and cell sizes. Quantitative transcriptomic analysis revealed a series of deferentially expressed genes (DEGs), all of which were up-regulated in granulocytes.