Genus Ipomoea is the largest of the family Convolvulaceae. It is a highly diverse genus distributed all around the world. In Sri Lanka, 13 members have been identified in Ipomoea; however, most of them have not been morpho-genetically characterized. In the present study, we selected I. batatas, I. aquatica, I. nil, and I. pes-caprae for the assessment based on certain criteria viz., food security, leafy vegetable, emergent weed, and coastal conservation capabilities. The morphological variation, species delimits, and phylogenetic relationships among these four species were assessed. The DNA was extracted from young leaf samples using CTAB method and subjected to PCR using ITS and rbcL as markers. The PCR products were subjected to sequencing. The DNA sequences were analyzed, and phylogenetic trees were generated by using PAUP to define the species delimits, identify the speciation and evolutionarily relationships in comparison to the homologous Ipomoea sequences available in GenBank. The tuber bearing ability, flower colour, and leaf shape are the key morphological descriptors that can be used to delimit the selected species. Both rbcL and ITS markers could be used to identify the four species studied distinctively. However, among the two markers, ITS provides a greater variation to identify the four species and their evolutionary relationships. Thus, the present study provides a key platform with usable morphological traits and DNA barcoding markers to characterize all Ipomoea species in Sri Lanka.