Passion fruit is a native fruit of tropical America, with Brazil being the world's leading producer and consumer of this fruit, with an estimated annual production of 554,598 Mg, and yield of 13,500 kg.ha-1 Phenotyping through digital images has been used to evaluate morphological characteristics of seeds. Knowledge of the degree of genetic divergence plays an important role, as it assists in the adoption of appropriate strategies for improvement in passion fruit populations.. The objective of this work was to estimate the genetic divergence among full-sibling families of passion fruit through morphophysiological characteristics of seeds using the Ward-Modified Location Model (Ward-MLM) method. Seeds of 98 full-sibling families (FSF) of passion fruit from the breeding program of the Mato Grosso State University were evaluated considering physiological descriptors of seeds, using germination and vigor tests; and morphological descriptors of seeds, using a digital imaging seed analysis device and software. We found that the Ward-MLM method was efficient in detecting genetic divergence using seed morphological and physiological descriptors, simultaneously. The descriptors that contributed the most to the genetic divergence among ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 18 (3): gmr18331 L.R. Fachi et al. 2 FSF were those related to seed geometry. This method formed three heterotic groups. Group II had the largest mean emergence speed index (1.106) and seedling emergence percentage (65.8%), and Group III had the largest means of seedling dry weight (4.140 g), radicle length (6.30 mm), germination speed index (2.503), and seed germination percentage (90 %). We conclude that crosses between FSF groups II and III are a good option to improve seed characteristics.