The genetic integrity of nine faba bean landraces and their regeneration groups were studied to investigate the effects of sample sizes and isolation methods on the regeneration of faba bean (vicia faba L.) using AFLP markers. Seeds stored in the national genebank were used as CK. The results showed that: compared with those of the control group, the number of polymorphic loci, percentage of polymorphic loci, effective number of alleles per locus, Shannon index, and genetic diversity index decreased in 50 and 20 plants groups, but the decline was greater in 20 plants group. Genetic similarity analysis and UPGMA cluster showed that the genetic similarity between CK and 50 plants group was higher than that between CK and 20 plants group. Cages isolation can reduce pollen contamination, but their genetic integrity was lower than that of the open pollination groups.