Cotyledons (embryonic leaves) in conifer trees form in a single ring, or whorl. The number of cotyledons is quite variable, commonly from 3 to 10, unlike flowering plants, which are classified as to whether they have one or two cotyledons. Our data indicate that cotyledon positioning has a radial component, for the ring position, and a circumferential component, for the between-cotyledon positioning within the ring, and that these have different dependences on polar transport of the growth regulator auxin. We present a two-stage reaction-diffusion mechanism as a framework for understanding these observations and early cotyledon morphogenesis.