We reported our preliminary study on mapping of the expressed sequence tag (EST) using single- stranded DNA conformation polymorphism (SSCP) on polymerase chain reaction (PCR) product. Five ESTs primer pairs, developed from nuclear genes including CAD(cinnamyl-alcohol dehydrgenase), CHS(chalcone synthase), NIR (nitrite reductase), ARA554 (cDNA expressed in differentiating xylem in Pinus taedae) and GS (glutamine synthetase), were selected to optimize the experimental protocol and generate mapping markers in the megagemtophytes from a single tree of Pinus massoniana. Our ultimate goal was to use SSCP approach to construct a transcriptional map for comparative mapping studies in P. massoniana. The efficiency to construct a transcriptional map in P. massoniana based on the published EST primer pairs derived from other pine species critically depended on the successful amplification of ESTfragments and the ratio of the heterozygous loci revealed in P. massoniana. In this study, 3 (60%) out of 5 tested EST primer pairs were succeeded in amplification, however, only 1 (20%) gene was heterozygous in the tested tree. The ratio of heterozygous loci detected in this study was similar to that revealed by anonymous marker in P. taeda. Therefore, a low efficiency would be expected if the map would be constructed using single pedigree. The segregation ratio of loci revealed by primer pairs would be higher if multiple pedigrees would be used. We proposed that consensus mapping approach based on multiple-pedigree should be used for EST mapping and therefore to increase the efficiency of EST mapping.