A set of three tomato chromosome 7 introgression lines (ILs) containing overlapping segments of Lycopersicon pennellii DNA was screened with a set of 10 EcoRI–MseI and 10 PstI–MseI AFLP primer combinations. A large number of markers were identified that mapped to one of the four regions of chromosome 7 defined by the set of three ILs. Because many of the identified markers have known map positions in three tomato reference maps, their location on the tomato genome could be verified. It was demonstrated that the three chromosome 7 ILs carried a chromosome 10 region harbouring a cluster of six AFLP markers that had not been detected before using RFLPs. The causes and implications of this observation are discussed.