Abstract: In this study, 453 892 Pinus ESTs were downloaded from GenBank, and these ESTs were assembled into 20 886 contigs(representing 20 886 unigenes of pines)with GS De novo assembler from roche, according to species, respectively. Searching by the Sputnik engine, 2 678 microsatellites were detected in the assembled contigs. It is noticeable that trinucleotide repeats were found to be the most abundant microsatellites in this database(accounting for 59.2%). By contrast, the richness of the other type of microsatellites were relatively low, with di-, tetra-, penta-nucleotide repeats accounted for 12.0%, 13.3% and 15.5% of the detected microsatellites, respectively. Dominance of triplet microsatellites in genes can be well interpreted by genetic codon selection, since triplet corresponds to the length of genetic codon. Insertion or deletion of integrate genetic codon influences the protein less slightly than the insertion or deletion of other types of repeats. Experimental results showed an overall amplification successful rate about 72.9% in P. massoniana. Subsequently, 155 successfully amplified primer pairs were tested for transferability across 14 pine species and in Douglas fir. This test yielded transferability rates over 71.0% across the 14 pine species, yet it was only 25.2% in Douglas fir. In genus Pinus, functional analyses indicated that genes with and without SSRs were significantly diverged in categories of symplast, virion and virion part classified by cellular component, in rhythmic process category classified by biological process, and in auxiliary transport protein category classified by molecular function.