According to commercial use, market demand and survival of wild resources, Bergenia crassifolia, B. scopulosa, B. purpurascens were selected for tissue culture in vitro and standardized propagation. ISSR markers were used to analyze the genetic stability of tissue culture plantlets. The optimal multiplication medium was MS medium supplemented with 0.01 mg·L^-1 NAA, 0.5 mg·L^-1 6-BA, and 2.0 mg·L^-1 Vc with shoot tips used as explants. The multiplication coefficients were 3.10, 2.50 and 2.10 for the three species, respectively. The suitable rooting culture medium was 1/2MS medium with 1.0 mg·L^-1 IBA and 2.0 mg·L^-1 Vc, and the rooting rates for the three Bergenia species were 85%, 80%, and 75%, respectively. The rooted plants were transplanted in a mixed medium of humus, yellow sand, and perlite with volume ratio 2:1:1; the survival rates of transplanted plantlets were 90%, 85% and 80%, respectively. Using this method of rapid propagation, three Bergenia species propagated 200 000, 20 000, and 10 000 plantlets, respectively. ISSR molecular marker detection results showed that genetic variation was greater for regenerated plantlets of B. purpurascens than the mother plant and was lower for regenerated plantlets of B. scopulosa than the mother plant. After 20 generations of regeneration, the plantlets of the 3 Bergenia species showed genetic variation. The average genetic variation rate of B. scopulosa and B. purpurascens increased with increasing subculture times, but the average genetic variation rate of B. crassifolia after the increase in number of generations changed irregularly.