The genetic diversity of 13 species Fontinalaceae collected in different regions was studied using ISSR marker technique method. The results showed that 526 clear bands were amplified by 7 stable and highly reproducible primers of which 518 were polymorphic. the percentage of polymorphic bands reached 98.47%. The result of analyzed by the software POPGENE-32 showed that number of alleles Na=1.7363, effective number of alleles Ne=1.3062. Nei gene diversity and Shannon information index were 0.201 5 and 0.321 1. It showed that the geographical distribution was very obvious. The coefficient of gene differentiation Gst, genetic distance D and genetic identity I of 13 samples were 0.025 3,0.007 1 and 0.054 7, indicating there was a certain gene flow among different species of Fontinalaceae and the genetic variation was mainly within species compared with interspecies. Cluster analysis among 13 samples genetic relationship using software NTSYS2.1 showed that these samples were divided into there groups. In addition ,there were some correlation between genetic distance and geographic distance among the samples.%利用ISSR分子标记方法对不同地区的13份水藓科植物进行遗传多样性分析，结果表明，稳定且重复性高的7条引物共扩增出526条清晰的条带，其中518条具有多态性，平均多态性位点比率为98.47％．运用PopGen-32软件分析发现，等位基因数Na=1.7363，有效等位基因数Ne=1.3062，Nei基因的多样性与Shannon信息的指数分别为0.2015和0.3211，说明水藓科植物的遗传多样性比较丰富．13份水藓科植物的遗传分化系数Gst、遗传距离D与遗传一致度I分别为0.0253、0.0071和0.0547，对其进行计算得知，不同属种间存有基因交流，但与种间变异相比，种群内部的遗传变异较大．通过NTSYS2.1软件对13份样本的亲缘关系进行聚类，可将其分为3类，且样本的遗传距离与地理位置有一定的相关性．
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