The morphology of female reproductive organs and anatomy, ultrastructure, and ultrasculpture of seed integuments were studied in more than 150 species of Podocarpales, Cephalotaxales, and Taxales. The main trends of morphological-evolutionary transformations of female fructifications were established in three studied groups of gymnosperms. The taxonomic weight of structural features of the female reproductive organs of Podocarpales, Cephalotaxales, and Taxales was determined. Seeds of 20 species of these orders were investigated using amino acid and Western blot analysis. The index of remoteness from the least specialized hypothetical taxon and degree of difference between taxa were calculated from data on amino acid composition of seeds and embryos. The differences in the degree of similarity between Podocarpales and other groups of gymnosperms were demonstrated. An original concept was proposed for phylogenetic relations between Podocarpales, Cephalotaxales, and Taxales.

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