Exploring patterns in the evolution of seed plant reproductive morphology within a functional context offers a framework in which to identify and evaluate factors that potentially drive reproductive evolution. Conifers are a particularly useful group for studies of this kind because they have a long geologic history and their reproductive organs are borne on separate structures with discrete functions. Multivariate analysis of morphological data collected from pollen-producing and seed-producing cones of Paleozoic, Mesozoic, and extant conifer species shows that seed cones underwent a significant expansion of morphological diversity that began during the Early–Middle Jurassic and has continued into the present day. In contrast, pollen cones show significantly lower levels of morphological diversity and exhibit similar basic morphologies throughout conifer evolutionary history. The increase in seed cone diversity through time is primarily the result of two novel structural and organizational features that evolved independently in different conifer families during the Mesozoic: robust, tightly packed cones in members of Araucariaceae, Cupressaceae sensu lato, and Pinaceae, and highly reduced, fleshy cones or solitary seeds in Podocarpaceae, Taxaceae, and some members of Cupressaceae sensu stricto. In extant conifers, these cone morphologies are associated with species that have strong interactions with vertebrate seed predators, seed dispersers, or a combination of both. This suggests that increases in the strength and complexity of biotic interactions in the Jurassic and Cretaceous were a primary driver of conifer reproductive evolution, and that patterns of character evolution relate to the increasing importance of cone tissue in seed protection and seed dispersal through time.