We report a method of microsatellite-anchored fragment length polymorphisms for DNA fingerprinting. The method combines the concept of AFLP and the microsatellite-anchor primer technique. Genomic DNA was digested by one restriction enzyme MseI. One AFLP adaptor (MseI adaptor) was ligated onto the restriction fragments. DNA fingerprints were produced by PCR using one microsatellite-anchor primer in combination with one MseI-primer. The method allows co-amplification of over 100 DNA fragments containing microsatellite motifs per PCR. Polymorphisms detected from lupin by this method included those arising from variation in the number of microsatellite repeat units targeted by the microsatellite-anchor primers, from variation on the annealing sites for the SSR-anchor primers, from insertions/deletions outside the SSR region, and from variation in restriction sites. The first three types of polymorphisms were readily converted into sequence-specific PCR markers suitable for marker-assisted breeding.