Using two sweetpotato (Ipomoea batatas (L.) Lam) F1 populations from diverse environments we investigated the AFLP marker profiles of the genotypes for association studies between the molecular markers and southern root-knot nematode (Meloidogyne incognita) resistance expression. Population one consisted of 51 half-sib genotypes developed at the Louisiana State Univ. AgCenter. The second population consisted of 51 full-sibs developed by the East African and International Potato Center sweetpotato breeding programs. Results for nematode resistance expression indicate a binomial distribution among the genotypes. Using analysis of molecular variance, logistic regression and discriminant analysis, AFLP markers that are most influential with respect to the phenotypic trait expression were selected for both populations. A comparative analysis of the power of models from the two statistical models for southern root-knot nematode resistance class prediction was also done. The diversity and possible universal similarity of influential markers between the two populations and the expected impact in sweetpotato breeding programs will be discussed.