Despite continued implementation of management strategies, the pathogen Ceratocystis fimbriata persists as a significant threat to the sweetpotato industry in the United States. The presence of few breeding programs, limited knowledge of the genetic basis of resistance, and hexaploid nature of the crop pose challenges to develop resistant lines. Plants possess an innate immune system with disease resistance R genes encoding for proteins that recognize pathogen effectors during infection. An important class of resistance gene contains nucleotide-binding and leucine-rich repeat domains, NLRs. We performed a protein motif-based search of NLRs in the diploid sweetpotato wild relatives I. trifida (NSP306) and I. triloba (NSP323) and compared the genome annotation with the annotation we conducted using NLR-parser. Our analysis revealed 121 and 117 complete NLRs in I. trifida and I. triloba respectively, while the original genome annotation had only identified 28 and 35 complete “NBS-LRR” sequences. Identified NLRs were used to design a bait-library to capture the NLR repertoire of sweetpotato using exome capture. Phylogenetic analysis of NLRs in sweetpotato, diploid wild relatives, and potato was also performed after annotating NRLs in genomes of white potato, peanut, cocoa, quinoa, strawberry, and lettuce. The identified NLR genes provide insight into the resistome of sweetpotato and a first step towards identifying Rgenes effective for control of C. fimbriata.