Genetic linkage maps of Tanzania and Bikilamaliya sweetpotatoes (Ipomoea batatas (L.) Lam), based on amplified fragment-length polymorphism (AFLP) were developed using a two-way pseudo-testcross. At a LOD score of 5, a total of 656 maternal and 469 paternal markers were ordered in 90 and 80 linkage groups, respectively, covering a total map length of 3655.6 cM for Tanzania and 3011.5 cM for Bikilamaliya. The average distance between markers is 5.9 cM, with only four intervals exceeding 30 cM. Mapping was carried out in two steps. Linkage among simplex markers provided a map framework to which multiple-dose markers were added. The maternal maps contained 91 duplex markers, which allowed identification of 13 homologous co-segregating groups; paternal maps contained 69 duplex markers, allowing identification of 10 homologous co-segregating groups. The exploitation of 215 double-simplex bridging markers detected 15 linkage groups as homologous maternal and paternal groups. Type of polyploidy (autopolyploidy vs. allopolyploidy) was evaluated using the ratio of repulsion to coupling linkages. The absence of linkages in the repulsion phase indicated a high level of polysomic inheritance of homologous chromosomes. The detection of a few repulsion linkages at a lower confidence level, however, demonstrated that there is partial preferential chromosome pairing in sweetpotato.