Lotus (Nelumbo nucifera) is an aquatic vegetable cultivated in Asia. Lotus rhizome rot is a sever disease that reduces productivity. We extracted and analyzed the compounds contained in the seed rhizomes of ‘Bicchu’ and ‘Lotus,’ cultivars that differ in resistance to rhizome rot. Interestingly, triglycerides were identified only in ‘Lotus,’ which exhibits a stronger disease resistance than ‘Bicchu.’ However, trilinolein, one of the major triglycerides in rhizomes, did not inhibit the growth of Fusarium commune isolated from rhizomes. Therefore, the differences in the rhizome lipid contents were unrelated to their resistance to rhizome rot. Although in this study we analyzed the major compounds in uninfected rhizomes, certain minor anti-fungal phytochemicals in disease-resistant rhizomes might be induced post-infection with pathogenic fungi. This cultivar comparison approach would be useful for further comprehensive studies on these phytochemicals.