AFLP is a PCR-based tool used in genetics research and DNA fingerprinting. Predicting the result and selecting the right primers play key roles in AFLP. Software called AFLP Runner (AR) was developed for AFLP predicting and analyzing. AR is a software based KMP algorithm for finding restriction enzyme cutting site sequence in genome. AR can be used for all organisms' AFLP primers selecting, bands information predicting and enzyme cutting site distributing. The accuracy of AR was tested using AFLP experiment of Nipponbare (O. sativa ssp. Japonica ) and the result show that result of AR was coincided well with the experiment.