In order to understand the genetic relationship of Morinda citrifolia (noni), the DNA fingerprints of 13 noni germplasm resources of were studied by ISSR markers. The results showed that ten ISSR primers could amplify 183 bands, of which 159 bands were polymorphic, accounting for 86.9%. The genetic similarity coefficients of 13 noni germplasm resources ranged from 0.464 to 0.784. Cluster analysis showed that 13 noni germplasm resources could be divided into two clads, in which Small fruit as a single group had distant relation with other germplasm resources. Although all noni germplasm resources could not completely separated according external morphological characteristics, the most with the same characteristics could be clustered into the same group or sub-group.