A new type of molecular marker, fluorescence-based AFLP, was evaluated for its ability to identify oilseed rape cultivars. Each of the six tested AFLP combinations detected polymorphisms, the best combination (MCAA/ E-ACT) had 26% of polymorphic peaks from a total of 90 peaks and could distinguish analysed cultivars, and 4 out of 5 DH lines. The results presented here show that florescence-based AFLP was, for the purposes of oil seed rape cultivar fingerprinting, a very suitable approach.
