R.A.H. Onsa, I. Ae. Abdellatif and M. Ge. OsmanIxora coccinea is one of the important ornamental plants, commercially propagated by stem cuttings. This study aims to determine the effects of different media on micropropagation and rooting and to investigate the genetic fidelity of regenerated plants using the Inter Simple Sequence Repeat (ISSR) marker. For this purpose, Murashige and Skoog (MS), and Woody Plant Medium (WPM) media were used for micropropagation and rooting experiments. All media were supplemented by 5.5g /l gelling agent (Agar) for micropropagation, MS media with different level of sucrose (15,30 ,45 and 60 g/l), 2.0 mg/l BAP with different concentrations of IBA (0.0, 0.1, 0.25 and 0.5 mg/l), for rooting 10mg /l NAA used. In vitro rooted plantlets were transferred to plastic pots containing; peat moss with vermiculite (1:1; 2:1, and 1:2 v/ v) for acclimatization to ex vitro conditions. The ISSR markers were used for the assessment of genetic fidelity between the mother plant and acclimatized plantlets ISSR marker used. Total DNA was extracted from leaves of the acclimated plant by the cetyltrimethyl ammonium bromide method (CTAB), and the data obtained were analyzed and used to generate a similarity matrix using Jaccard’s similarity coefficient. The best result in terms of regeneration of shoots was obtained from 30 g/ l sucrose on a full MS medium. MS media during the incubation period gave the best results in terms of vegetative growth parameters compared to WPM. The estimation of the genetic similarity coefficient based on the ISSR band indicated that acclimatized plantlets derived from the 6th subculture were 100% similar to the mother plant.