Citrus rootstocks are essential in the citrus industry because they affect more than twenty agronomic characteristics of the citrus and fruits. Characterization and documentation of germplasm bank introductions allow to avoid duplicates and to identify promising accessions for selection processes, breeding or agro-industrial processes. It was evaluated the genetic diversity of 39 accessions from the citrus rootstocks germplasm bank of the Colombian Corporation for Agricultural Research (Corpoica-Palmira). Six RAMs primers were used which generated 134 polymorphic loci that were used to estimate genetic diversity parameters. Expected heterogeneity and polymorphic loci percentage for the collection was 0,38 and 92,54%, respectively. Similarity analysis allow to appreciate that the materials are dispersed in the dendrogram, however a similarity level of 0,63 grouped the accessions of the genus Poncirus and their hybrids. The species Clausena lansium was the most distant from other species in the dendrogram and differed at a similarity level of 0,54. The results indicate a high genetic diversity in the citrus rootstocks germplasm bank of Corpoica that can be used in future research programs.