<p>Several Convolvulaceae species harbor heritable fungal endophytes from which alkaloids are translocated to reproductive tissues of the plant host. Evidence for the distribution and ecological role of these fungal alkaloids, however, is lacking or incomplete for many host species and growth forms. Here we report on the identity of the fungal endophytes and quantities of alkaloids present in the leaves and seeds of the arborescent morning glory, <i>Ipomoea murucoides</i> (Convolvulaceae). Young folded leaf samples taken from the wild, harbored mycelium of one of two fungal taxa wrapped around the leaves’ glandular trichomes. Most trees harbored the swainsonine producing <i>Ceramothyrium</i> (Chaetothyriales) fungi while a few trees were found to harbor a <i>Truncatella</i> (Xylariales) species, suggesting endophyte replacement. Seeds had higher concentrations of the indolizidine alkaloid swainsonine than leaves. Additionally, seeds from trees harboring <i>Ceramothyrium</i> fungi exhibited less bruchid damage and had higher concentrations of swainsonine than seeds from trees harboring <i>Truncatella</i> fungi. Five sesquiterpenes were detected in the leaf trichomes in both <i>Ceramothyrium</i> and <i>Truncatella</i> colonized trees. The seed content of the tropane alkaloids, tropine and tropinone, did not differ significantly among the two fungal symbionts. It is likely that the host allocates the defensive chemicals from leaves to seeds, protecting them from seed predators such as bruchid beetles. Overall, our field data show that <i>Ipomoea</i> species provides an interesting opportunity to study vertical and horizontal fungal symbiont transmissions.</p>