Molybdenum (Mo) is considered and described as an essential element for living organisms’ development. Until now, no studies have been performed on genes involved in the Mo transporter in ancestral Ipomoea species. This study aimed to identify potential Mo genes in Ipomoea trifida and I. triloba genomes using bioinformatics tools. We identified four Mo transporter genes, two in I. trifida and two in I. triloba. Based on the RNA-seq datasets, we observed that Mo genes are expressed (in silico) and present different mechanisms between the tissues analyzed. The information generated in this study fills missing gaps in the literature on the Mo gene in an important agronomic crop.