Tembesu (Fagraea fragrans Roxb.) is a multipurpose indigenous species in Indonesia that can grow well on various types of site, such as in the dry land, temporary waterlogged or permanent waterlogged land. The purpose of this study was to examine the morpho-physiological characteristics of leaves, fruits, and seeds of tembesu from five populations in South Sumatra and Western Java. Analysis of variance with completely randomized design was used to discern the characters among the five populations (Kemampo, Sungai Pinang, Kota Raya, Dago, and Carita). The results showed that all of the morpho-physiological characteristics of leaves, fruits, and seeds were significantly different among populations. Severalvariables of agro-climate significantly correlated with leaves, fruits, and seeds characteristics indicating the environment's influence. Most of the charaters had higher environment coefficient of variances than genotypic coefficient of variances which revealed a high environment contributions. Based on the characteristics of leaves, fruits, and seeds, the populations can be grouped in two, i.e. the first group consisted of the population from South Sumatra (Kemampo, Sungai Pinang, Kota Raya) and the second group from the population of Western Java (Dago and Carita). The investigation has important practical implications for genetic resources management and future breedingprograms of tembesu.