Pinctada martensii is an important cultured marine mollusc in the southern China. In order to draw up tissuespecific gene expression map, nine cDNA libraries of P. martensii, including blood, foot, gill, stomach, liver, heart, mantle,pearl sac and Polydora ciliata infected blood, were constructed. Total ly 6979 ESTs were obtained by sequencing clones from these cDNA libraries. Thoroughly screened with the software of Misa, at a criterion of at least 5, 4, 4, 4, 3 to the copy level of di, tri, tetra, pentra, hex motif respectively, a total number of 268 simple repeat sequences were found. 243 ESTs (3.48%) have at least one microsatellite repeat. Among these 9 cDNA libraries, 6.16％ pearl sac ESTs, the highest, contain microsatellite, while the lowest, 1.65%P. ciliata infected blood ESTs have at least one microsatellite. In the 268 repeat sequences, the number of the dinucleotide repeats is 130，about 48.5%, and the most among all of the repeat sequence s. (AT/AT)n, the most, account for 29.1% of total repeat sequences. The second is the trinucleotide repeats, 83, almost 31%. More than 50% are the two most abundant trinucleotide repeats types of (AAT/ATT)n and (AAG/CTT)n. The third is the tetranucleotide repeats, 30(11.2%), and (AAAT/ATTT)n nearly reaches 50% of tetranucleotide repeats. Primers can be designed in 151 microsatellite containing ESTs. 130 pairs of primers, about 86.09%, could be amplified in P. martensii DNA. There was no difference of microsatellite containing EST ratio among plasmid libraries and phage libraries. However, libraries constructed with ZAPcDNA synthesis method have much higher ratio of microsatellite containing EST than those with SMART cDNA. 45 EST-SSRs were confirmed to be polymophic by PCR and PAGE electrophoresis in 8 individuals, 4 each from Sanya population and Indian population respectively. Thesepolymophic ESTSSRs will be useful for molecular genetics study，identification and wild resource conservation.