Durio zibethinus, known as durian in several Southeast Asian countries, is a prospective horticultural commodity to cultivate and develop. This study aimed to determine the phenotypic diversity and relationship of superior durian varieties from South Kalimantan in Indonesia based on morphological characteristics. Here, 20 varieties of durian (D. zibethinus), including an outgroup, were used. Meanwhile, 57 morphological characteristics, comprising 35 qualitative and 22 quantitative, were observed. The Shannon index (H’) method was applied for phenotypic diversity, and the relationships were by the UPGMA. The results show that durians of the region have low phenotypic diversity. However, some morphological characteristics show high ones, e.g., crown shape, fruit skin color and thickness, fruit flesh thickness, and fruit spine length, including tree age. In this case, the highest fruit skin and flesh thickness are present in Malutu and Bamban Birin, respectively. In addition, the fruit spine length and tree age are also in ‘Malutu’. The UPGMA revealed that the durians were separated into seven clusters and near-corresponding to geographic origin. In this case, ‘Gentarbumi Uya’ is the closest to ‘Taradak Uya’, whereas the farthest is ‘Malutu’ with ‘Tapai Idaman’. Thus, this information is essential in promoting the future durian-breeding program in local and global coverages.