Rubber tree is the major commercial source of natural rubber, which is used in manufacture worldwide. Recent breeding program aims to provide a genetically superior planting material which has high latex production and better wood production. Marker assisted selection can improve breeding efficiency by enabling the direct selection of targeted genotypes. This study emphasizes on new expressed sequence tag-simple sequence repeats (EST-SSR)markers which were developed from ESTs of differentially expressed genes of inner bark and latex samples of high and low yielding clones of rubber tree. Sets of  polymorphic EST-SSRs from rubber tree have been published from many researchers, but none has been specifically developed to study on latex and wood yield traits. In this study, a set of 20 EST-SSR primers were selected to evaluate the genetic diversity in 34 rubber tree clones and 3 cassava varieties. All of markers revealed specific polymorphic patterns to rubber tree clones. The functional markers related with latex and wood yield were discussed and demonstrated to be able distinguish between high latex and high wood yield rubber tree clones. These potential functional ESTs and EST-SSR markers should facilitate genetic mapping, genetic diversity study and marker assisted selection in rubber tree breeding program.