Canna, the solitary genus of family Cannaceae, represents a group of ornamental plants species. In this investigation an attempt was made to access the genetic relationship among six species and varieties of Canna using RAPD and ISSR techniques. A total of 49 major scorable bands ranging from 200 to 1500 bp were generated from two RAPD and three ISSR primers showing 83.6% polymorphism. Generally low relationship between tested cultivars/species; and the highest correlation (5.09) was found between Canna lily (C3) and Canna indica red (C2) and between Canna flaccida (C5) and Canna indica red(C2). However, the lowest (3.316) similarity was observed between Canna lilyred brilliant (C4) and Canna flaccida (C5).  The dendrogram based on the contained data of both RAPD and ISSR which showed that Canna paniculata (C6) was always in a far correlation with the other species and varieties in this study. It was observed that the used primers of both RAPD and ISSR divided the plants according to the flower colour with ignorance to the leaves colour and grouped (C. variegata, C. indica redand C. paniculata)together in one cluster, but in the other cluster, the primers grouped them according to the leaves cluster with ignorance of the flower colour (C. flaccida, Canna lilyredbrilliant and Canna lily). Finally, it might be the same cultivars grouped in other way in case of using other primers or other molecular marker system.