Genetic diversity and genetic structure of wild banana resources from watershed in Fujian province were examined by ISSR. The results showed that: 117 bands were amplified with 12 ISSR primers, polymorphic bands of which were 105, and their polymorphism percentage was 89.7%. The Nei’s genetic distance was 0.244, the Shannon’s information index was 0.381, the genetic diversity in different natural populations has significant difference and the Sanming wild banana was higher. The coefficient of gene differentiation was 0.589, gene flow was 0.349, the genetic differentiation among the populations was higher than that within the population. The clustering result based on Nei’s genetic distance was the same as model-cluster-method, the banana resources were clustered into 3 groups, including Sanming wild banana group in Shaxi tributary, Nanping wild banana group in Minjiang upstream and nearby tributary, and Fuzhou wild banana group in Minjiang downstream group. The results indicated that the rich genetic diversity comes from the high frequency of heritable variation among national populations that resulted from heterogeneous habitats in Minjiang watershed. The genetic diversity and genetic divergence of Sanming wild banana group was the highest, and it may be the original center of Fujian wild banana resources, which was also the most important community to utilize and protect. In addition, water was a key factor of genetic transfer in Minjiang watershed.