Various Hibiscus species such as Hibiscus rosa sinensis linn, Hibiscus malvaviscus arboreus, Althaea rosea, Hibiscus rosasinensis sp., Hibiscus schizopetalus, Hibiscus china rosa, Hibiscus sabdariffa L. and Hibiscus cannabinus L. (kenaf) were collected from Antoniades Gardens in Egypt. These species were very similar in the morphology of the flowers and leaves, thus morphological markers traits use to identify these different Hibiscus species is limited and less accurate because they are strongly influenced by environmental conditions. Therefore, using molecular markers of DNA for plants is considered to be more accurate than morphological markers. In this study we used eight primers from (RAPD), five (ISSR) primers, and four (SSR) primers for the analysis on these species of Hibiscus. The results showed for all primers were as follows; the total number of the polymorphic fragments of RAPD, ISSR and SSR were 89, 72, and 15; respectively, with an average polymorphism about 97.75%, 98.61%, and 100%, respectively. Moreover, the dendrogram for the phylogenetic tree analysis of RAPD was divided into two main clusters, the first cluster has C7 (Hibiscus sabdariffa L), and the second cluster comprised the other species. For ISSR phylogenetic analysis, the dendrogram was divided into two main major clusters, the first cluster had C3 (Althea rosea), C7 (Hibiscus sabdariffa L.), and C8 (Hibiscus cannabinus) and the second cluster comprised the other species. Whereas for SSR phylogenetic analysis, the dendrogram was divided into two main major clusters, the first cluster had C2 (Hibiscus malvaviscus arboreus), and the second group comprised the other species.