Storage roots are an important adaptation to harsh environmental conditions. The number of plant species with storage roots is not known, likely because storage roots are difficult to study. Many species distributed across the morning glory family, Convolvulaceae, form storage roots, including sweetpotato, Ipomoea batatas (L.) Lam. I employed a comparative approach to investigate the evolution and development of storage roots in morning glories. We first estimated relationships among major morning glory linages using plastome sequences to examine the evolution of three ecologically important traits: storage roots, flower color and ergot alkaloid presence. We then used target enrichment to estimate relationships in the sweetpotato complex, as well as the timing and extent of hybridization. While accounting for phylogenetic relatedness among species, we tested for a correlation between polyploidy and root traits in the Batatas complex. Finally, we examined anatomical and transcriptomic changes associated with storage root formation in two pairs of distantly related morning glory species. These findings suggest numerous independent origins of storage roots throughout morning glory evolution. Within the Batatas complex, phylogenomic analyses revealed ancient hybridization with minimal evidence for ongoing gene flow. In addition to the possibility that hybridization among unrelated lineages has led to introgression of loci controlling storage root formation and the origin of storage roots, polyploidy may have also played a role. This hypothesis was tested, and we found that ploidy level and genome size were poor predictors of storage root formation. Therefore, factors other than whole genome duplications are needed to explain root trait diversity in the Batatas complex. Finally, comparative anatomical and transcriptomic analyses revealed that storage roots of sweetpotato and Merremia dissecta, two distantly related morning glory species, utilize a common core set of genes in storage root formation despite exhibiting different storage root developmental patterns. Many of the genes showing increased expression during storage root formation are involved in the starch biosynthesis and others are regulators of starch synthesis and cambium formation. Taken together, the results support a multifaceted picture of storage root evolution and development, suggesting this is a complex morphological trait with numerous evolutionary origins.