The number of cotyledons in angiosperm monocots and dicots is tightly constrained. But in the gymnosperm Pinaceae, including conifers, cotyledon number (n c ) can vary widely, commonly between 2 to 12. Conifer cotyledons form in whorled rings, on a domed embryo geometry. We measured embryo diameters and counted cotyledons to determine the radial positioning of the whorl and the circumferential spacing between cotyledons. Results were similar between Douglas fir (Pseudotsuga), Sitka spruce (Picea) and larch (Larix), indicating a common mechanism for cotyledon positioning in conifers. Disrupting transport of the growth regulator auxin (with NPA) led to cup-shaped embryos, indicating that whorl (ring) formation is separable from cotyledon patterning within the ring. NPA inhibits cotyledon outgrowth, but not the spacing (distance) between cotyledons. The NPA effect is direct; it does not operate indirectly on embryo size. These results support a hierarchical model for cotyledon positioning in conifers, in which a first stage (not requiring auxin transport) sets the whorl position, constraining the second stage (which requires auxin transport) to form cotyledons within this whorl. Similarly, recent studies in Arabidopsis have shown that different components of complex developmental patterns can have different transport properties; this aspect of patterning may be shared across plants.