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Phenotyping through digital images has been used to evaluate morphological characteristics of seeds, providing fast, accurate results. 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-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 seed analysis device. The Ward-MLM method was used to quantify genetic divergence. The study showed 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 FSF were those related to seed geometry. The Ward-MLM method formed three heterotic groups. Group II presented higher means of emergence speed index (1,106) and seedling emergence percentage (65.80%), and Group III presented higher means of seedling dry weight (4,140), radicle length (6.30), germination speed index (2,503), and seed germination percentage (90.00). These results show the possibility of crosses between FSF groups II and III as a viable alternative to improve seed characteristics.