AFLP is a method for genotyping individuals for a large number of loci using a minimal number of PCR reactions. The method is based on Vos et al. 1995 (AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407-14. There are three key steps to the method.

1. DNA is cut with restriction enzymes and then linkers are ligated on. Typically this involves a combination of two restriction enzymes: a 4 base cutter (MseI) and a 6 base cutter (EcoRI).

2. Pre-selective PCR is performed using primers which match the linkers. These primers have a two base overhang. Each combination (two bases on the MseI linker and two bases on the EcoRI linker) reduces the number of DNA fragments by 256.

3. Selective PCR is performed using primers with three base overhangs. For any given pre-selective amplification, there are 16 possible selective primer combinations that can be used. The EcoRI primer is labeled so that only fragments that contain an EcoRI site will be detected.

PCR products are then analyzed by gel or capillary electropherisis. Fragments are binned and then analyzed for fingerprint similarity with other samples.