I send you attached a paper on Crepidula fornicata's genetic polymorphism. The authors use AFLP to detect polymorphis although it had a limited capacity to detect variation in a small time scale (maybe less than 100 years). In addition, I attach also a paper that discuss critically the approach of AFLP versus others (RFLP) .Maybe from these papers you may find out which will be the best approach in your case. AFLP seems to be less time consuming. Hope it helps. Regards, Alexandra