Abstract: The transferability of Pinus yunnanensis EST-SSR markers to different populations of P. yunnanensis and its related species was studied by 7 SSR primers randomly selected 32 SSR primers, which were designed based on ESTs. Polymerase chain reaction (PCR) to genomic DNA from P. yunnanensis、P. yunnanensis var.tenuifolia、P. massoniana、P.densata、P. tabulaeformis and P. kesiya var. langbianensis were tested using 7 SSR primers. The amplification percentage of selected primers to different populations of P. yunnanensis and its related species were 100%. The percentage of polymorphism of 7 SSR primers was 100% of different populations in P. yunnanensis, and its related species were 7143%, 8571%, 8571%, 8571% and 100%, respectively. These results indicated that the P. yunnanensis EST-SSR marker was highly transferable to its related species, and these primers can be used to analyze the genetic relationship between the P. yunnanensis and its related species. This study effectively proved that EST-SSR from P. yunnanensis was valuable for genetic analysis and linkage mapping study among P. yunnanensis and its related species.