Restriction fragments of the genomic DNA are produced by using two different restriction enzymes: a frequent cutter (the four-base restriction enzyme MseI) and a rare cutter (the six-base restriction enzyme EcoRI). The frequent cutter serves to generate small fragments, which amplify well and which have the optimal size range for separation on a sequence gel, whereas the rare cutter limits the number of fragments to be amplified.
By using two enzymes you get enough (size-) polymorphic fragments that are still small enough to amplify and to detect them on a scanner in a large number.