The sporangia of vascular plants are technically asexual, but in the seed plants, because the gametophytes are wholly dependent upon the sporophyte and the female gametophyte even remains within the megasporangium, sexual terminology continues to be erroneously extended to the sporophyte and sporangium-bearing organs. In all conifers the organs containing microsporangia (“male”) are separate from those bearing megasporangia (“female”), and in Cephalotaxus, some junipers (Juniperus), and the family Taxaceae they are found on different individuals.

The microsporangia of all conifers are attached to the scales of a simple pollen cone, or microstrobilus. The pollen cones usually consist of thin, parchmentlike scales (microsporophylls), each carrying two or more microsporangia on the lower surface. The number of scales and their size is quite variable, so that the overall length of the microstrobilus ranges from about 2 mm (0.08 inch) in some cypress (Cupressus) species to more than 20 cm (8 inches) in some Araucaria species.

Wide variations in the female (megasporangiate) reproductive structures among the conifers are the main basis for their classification. Most living conifers have a seed cone that is interpreted as a compound strobilus; each cone scale, inserted in the axil of a bract, is equivalent to an entire simple pollen cone. Fossil evidence shows how each ovule-bearing dwarf shoot of ancestral conifers was reduced and fused to form a single cone scale. Like the leaves, the bracts and scales are spirally arranged or occur in pairs or trios on the axis, and modern conifers have at least some fusion between each bract and its scale. The bracts and scales, or combined scales, vary in texture from woody to leathery, or even fleshy in bird-dispersed junipers (Juniperus) and the family Podocarpaceae. The number and size of cone scales varies widely among conifers, leading to seed cones that range from 3 mm (0.1 inch) long and less than 1 gram (0.04 ounce) in Microbiota of the Amur region of Russia to more than 40 cm (16 inches) long in the sugar pine (Pinus lambertiana) of California and more than 2.2 kg (4.9 pounds) in some Araucariaceae and the coulter pine (Pinus coulteri) of California.

The megasporangiate strobili of Cephalotaxus and most Podocarpaceae have the same basic structure as other conifer cones, but are so reduced and dominated by their much larger seeds that they do not look like cones. Even greater modification in the family Taxaceae has completely eliminated any trace of strobilar organization, and the solitary seeds sit at the tip of a short branch in a fleshly aril, a cup-shaped outgrowth of the seed stalk.

Distinguishing taxonomic features

Extant conifers differ from other gymnosperms in combining simple pollen cones with compound seed cones (or solitary terminal seeds in family Taxaceae). Although not possessed by all species, only conifers have needle leaves (of a variety of shapes) and pollen with bladders. Some other features, although not exclusive to conifers, are also more common in them than in other gymnosperms. Those include flattened, winged seeds (also in Welwitschia), scalelike foliage leaves (also in Ephedra), and the growth habit of a normal tree or shrub (also in Ginkgo).