Croton (Codiaeum variegatum (L.) A. Juss.) is one of the Euphorbiaceae family, and represents a group of ornamental plants. This species possesses a wide range of variations in colour and leaf shape. In the present study, six cultivars of croton were used to assess the genetic relationship among them by using ISSR and RAPD techniques. The results generated 53 total bands from three ISSR and RAPD primers. Also, it ranged from 200 to 2000 bp. with 92.4% polymorphism. The relationship between the used cultivars showed that (5.48) considered the highest relationship between Codiaeum variegatum ^‘Ptra' (C3) and Codiaeum variegatum ‘Victoria Gold Bell' (C1). However, the lowest similarity (1.57) was recorded between Codiaeum variegatum ‘Victoria Gold Bell' and ‘Yellow Lecton' (C6). The dendrogram depended on the achieved results which were generated from ISSR and RAPD primers. It divided the plants according to the leaf color with ignorance of leaf shape and size. It grouped ‘Ptra' (C3) and ‘Victoria Gold Bell' (C1) together in one group, but in the second group, the primers grouped ‘Sunny Star' (C2), ‘Gold Dust' (C5), var. pictum (C4) and ‘Yellow Lecton' (C6) together. It should be mentioned that it can obtain different results in the dendrogram when using another molecular marker system.