Amplified fragment length polymorphism (AFLP) markers linked to the stem nematode resistance gene were developed in sweet potato (Ipomoea batatas (L.) Lam.). Using bulked segregant analysis (BSA), 800 AFLP primer combinations were screened in the resistant and susceptible bulked DNA from the 186 progeny of an F1 single-cross population of Xu781 (resistant parent)×Xushu18 (susceptible parent), and 245 of these AFLP primers showed polymorphic bands between resistant and susceptible DNA. Primer combinations detecting polymorphism between the two bulks were used to screen the parents and eight individuals from each of the bulks. The results showed that E2M23 and E33M20 produced a specific band of about 500 bp and 200 bp in length, respectively, in the resistant plants but not in the susceptible plants, suggesting that the markers named E2M23500 and E33M20200 linked to a gene for stem nematode resistance. Amplified analysis of the 186 F1 individuals indicated that the genetic distance between these two markers and the stem nematode resistance gene was 6.9 cM and 11.1 cM, respectively, measured with Mapmaker 3.0. These two AFLP markers were used to identify ten sweet potato varieties planted widely in China and the results were consistent with those of conventional resistance identification, indicating that the two markers can be used in molecular marker-assisted breeding for stem nematode resistance in the sweet potato.