<p>The root-knot nematode (<i>Meloidogyne incognita</i>) represents a significant threat to <i>Ipomoea batatas</i> (sweet potato) cultivation. Breeding efforts over the past decades have focused on the development of resistant cultivars, resulting in the identification of several genotypes exhibiting varying degrees of resistance. A prior study focusing exclusively on Korean cultivars identified two genes, AT4G16620 and AT5G66430, as being associated with nematode resistance. However, that analysis was conducted using an outdated genome assembly, which did not account for the hexaploid nature of the <i>I. batatas</i> genome, potentially limiting the resolution of genetic associations. Furthermore, numerous non-Korean cultivars exhibiting diverse resistance phenotypes have yet to be genetically characterized. To elucidate the genetic basis underlying nematode resistance, we analyzed whole-genome resequencing data from thirty-one <i>I. batatas</i> cultivars with well-characterized nematode resistance profiles. Comprehensive in silico analyses revealed the presence of three distinct genetic clades, each associated with differential resistance levels to <i>M. incognita</i>. Subsequent variant analysis identified putative causative mutations unique to each clade, offering insights into the molecular mechanisms of resistance. These findings provide valuable targets for the development of resistant cultivars and inform future breeding strategies aimed at mitigating root-knot nematode infestations.</p>