Ergot alkaloids are mycotoxins that can increase host plant resistance to above- and below-ground herbivores. Some morning glories (Convolvulaceae) are infected by clavicipitaceous fungi (Periglandula spp.) that produce high concentrations of ergot alkaloids in seeds-up to 1000-fold greater than endophyte-infected grasses. Here, we evaluated the diversity and distribution of alkaloids in seeds and seedlings and variation in alkaloid distribution among species. We treated half the plants with fungicide to differentiate seed-borne alkaloids from alkaloids produced de novo post-germination and sampled seedling tissues at the cotyledon and first-leaf stages. Seed-borne alkaloids in Ipomoea amnicola, I. argillicola, and I. hildebrandtii remained primarily in the cotyledons, whereas I. tricolor allocated lysergic acid amides to the roots while retaining clavines in the cotyledons. In I. hildebrandtii, almost all festuclavine was found in the cotyledons. These observations suggest differential allocation of individual alkaloids. Intraspecific patterns of alkaloid distribution did not vary between fungicide-treated and control seedlings. Each species contained four to six unique ergot alkaloids and two species had the ergopeptine ergobalansine. De novo production of alkaloids did not begin immediately, as total alkaloids in fungicide-treated and control seedlings did not differ through the first-leaf stage, except in I. argillicola. In an extended time-course experiment with I. tricolor, de novo production was detected after the first-leaf stage. Our results demonstrate that allocation of seed-borne ergot alkaloids varies among species and tissues but is not altered by fungicide treatment. This variation may reflect a response to selection for defense against natural enemies.