Ontogenetic shape change has long been recognized to be important in generating patterns of morphological diversity. Here we explore how patterns of seed cone disparity change over ontogeny across the Cupressaceae conifer clade by comparing two end-member developmental stages: pollination and seed maturity. We sampled cones at pollen release and just prior to seed release, measuring basic morphometric shape variables of their bract-scale complexes (length, width, thickness). We then used several multivariate statistical methods to characterize patterns of morphospace occupation; in particular, we used a hypervolume method to quantify percentage overlap in morphospace among taxa at pollination and maturity. We found that bract-scale complexes at both pollination and mature stages exhibit substantial variability, but morphospace occupation is more discretized at maturity, such that taxa occupy less of the aggregate hypervolume and show less overlap with other taxa. This pattern results from two cone growth strategies that generate two distinct shapes of bract-scale complexes; relatively thin laminar scales that imbricate to enclose seeds and relatively thick, peltate scales that interlock to enclose them. By contrast, pollination-stage bract-scale complexes all exhibit laminar shapes and different taxa occupy slightly different positions within a broad cloud of variability. The two growth patterns occur across lineages, suggesting multiple shifts in growth strategies among clades. The morphological diversity observed among mature cones therefore largely happens post-pollination in Cupressaceae due to different strategies of cone growth that seal off seeds in divergent ways. These results highlight how morphological diversity in seed cones reflects the evolution of disparate trajectories of ontogenetic shape change, even if the ultimate functional role of the cones remains similar.