Amplified fragment length polymorphism (AFLP) analysis, a genetic fingerprinting technique based on polymerase chain reaction (PCR), can present financial and logistical challenges, as the use of radioactive isotopes and sequencing gels can be dangerous and expensive. Our goal was to optimize an AFLP protocol that did not require these materials and could distinguish among clone lines of pale anemones (Exaiptasia pallida). Anemone DNA was digested with EcoRI and MseI endonucleases. Adapters were ligated to cut sites, and fragments were amplified via nested PCR using increasingly selective EcoRI- and MseI-specific primers. In the final amplification step, EcoRI primers were labeled with 5(6)-carboxyfluorescein (FAM). Amplified fragments and a FAM-labeled ladder were electrophoresed through pre-cast polyacrylamide mini-gels. Gels were photographed and bands were marked manually. Fragment lengths were determined by comparison with the FAM-labeled ladder. Estimates of genetic similarity were then calculated for each pair of fingerprints using the Jaccard index of similarity, S_J. Samples were clustered on a dendrogram into five significantly different groups using similarity profile (SIMPROF) analysis. Comparisons of sample replicates yielded a mean S_J of 0.74, and mean S_J values within groups ranged from 0.51 to 0.72. Our safe and cost-effective genetic fingerprinting method was used to distinguish among E. pallida clone lines without the use of radioactive isotopes or sequencing gels. As E. pallida is increasingly used as a model for studying the establishment, maintenance, and breakdown of the symbiotic relationship in cnidarians, our protocol facilitates genetic fingerprinting of this vulnerable lineage of marine organisms.