Plants are one of the main food sources , which also include bioactive compounds for maintaining human health. Diospyros lotus L. is an economically important species with the edible fruits and valuable timbers. The leaves, fruits and seeds of the plant are used in folk medicine. The aim of this research was to study morphological characteristics of seed and seed weight of D. lotus, collected from natural ranges of the species in the northwest and southeast of Azerbaijan in 2016, 2018 and 2020. We have selected five morphological characteristics of seed: length, width,  area, minimum circumscribed, and perimeter. The results showed that the most of the seeds examined have medium size with the following length, width and area ratios: 9.26-11.65 x 5.05-6.44 x 42.00-63.81 mm. Variability of fruit size in the population calculated from 2.2 cm to 0.97 cm. Moreover, D. lotus is an endangered species in the country within its natural habitat and is included in the Red Book of Azerbaijan. Given the current decline in the wild populations of this species in its natural area distribution, both regionally and globally, implimentation of appropriate studies is important. Morphological variability and differences of seeds can also directly influence their ability to germinate, which is very important for the conservation of the species. Current research could be also useful for the analysis of taxonomic relationships, which may provide some important data for understanding the phylogeny and status of studied taxa.