This paper introduces an integrated system of morphological concepts for gymnosperm fructifications, which does not lean upon any system existing for other higher plants. Comparative analytical treatment of all available characters of the most thoroughly studied fossil genera provided the foundation for an ordered ranking of congregations, each unit being assigned to the status of families, orders and classes. The transformation of the generative and vegetative organs has been traced along various phylogenetic branches. A new large phylogenetic branch (class Ginkgoopsida), beginning with the Lower Carboniferous Calamopityales, has been established. The lineage evolved from this order to Callistophytales and further to Peltaspermales. The family Peltaspermaceae encompasses, among others, plant types formerly regarded as ginkgoaleans. The orders Ginkgoales, Leptostrobales (Czekanowskiales) and Caytoniales evolved from the Peltaspermales. The order Arberiales (glossopterids) evidently evolved from the Calamopityales. In the lineage from Calamopityales to Ginkgoales a common seed type is conserved (platyspermic, non-cupular with two vascular bundles in the integument). Radiospermic seeds are conserved in the class Cycadopsida. In the lineage from Lagenostomales to Trigonocarpales the radially symmetrical cupule underwent modification into an integument of the same type of symmetry. The earliest Lagenostomales with the bilaterally symmetrical cupule evolved into the Cordaitanthales, where the cupule, also undergoing modification, was transformed into a bilaterally-symmetrical integument. In Cordaitanthales and their descendents the Pinales the seeds became secondarily platyspermic (in contrast to the primary non-cupular and primary platyspermic seeds in Ginkgoopsida); their vascularization was progressively reduced. These two orders are grouped into the class Pinopsida. It is believed that angiosperm seeds are in effect radiospermic with a radial cupule, their vascularization also being progressively reduced. If this holds true, the angiosperm ancestry should be sought in the class Cycadopsida. The Caytoniales, Arberiales, Peltaspermales, Leptostrobales and other orders of the class Ginkgoopsida should be excluded from the stock of probable angiosperm ancestors. A new gymnosperm phylogeny has been proposed and the evolution of the phylogenetic branches outlined in terms of the phytochoria system of the geological past. The basic evolutionary innovations took place within the Equatorial Belt and adjacent ecotone areas. Three types of processes, often underrated, have a paramount role in gymnosperm phylogeny. They are defined as follows: (1) homoeotic transformations of organs; corresponding to them are heterotopies, in the morphological aspect, and saltations, in the evolutionary sense; (2) dedifferentiation of the organs (the shift of one ontogenetic program onto various organs); (3) transitive polymorphism (conservation in diversity of a certain organ during phylogeny). These processes probably serve to indicate that rearrangement in the functions of the regulatory genes played an important role in the evolution of gymnosperms.