Mangrove habitats are important ecosystems for their ecological value and the goods and services they offer. The black mangrove Avicennia marina (Forssk.) Vierh. (Avicenniaceae) populations growing in the Nabq protected area represent the northernmost latitudinal limit of the Indo-Pacific-East African naturally growing mangrove forests. In this study, nine A. marina populations inhabiting Gulf of Aqaba were studied to assess the genetic relationship among the populations by Start Codon Targeted (SCoT) and Inter Simple Sequence Repeat (ISSR) as DNA Markers. Variations of photosynthetic pigment content were assessed in the populations growing in different habitat types. The numbers of polymorphic bands were 18 and 6 for SCoT and ISSR, respectively. The percentage of polymorphism showed a wide range amounting to 40.9 for SCoT and 25 for ISSR, while the number of amplicon bands ranged from 8–10 in SCoT and 2-9 in ISSR. The genetic relationships among populations using SCoT and ISSR analysis showed a close relationship between the nearby but different habitat types populations such as sand mound and littoral populations, or between populations of the same habitat types in the study region. The photosynthetic pigment content of chlorophyll a and b, and carotenoids in the littoral and intertidal populations were higher than that in the sand mound and salt plain populations. Populations inhabiting the Nabq protected area have a wide range of polymorphism among different habitat types. Further studies are required to investigate the genetic relationships among populations of A. marina inhabiting the eastern and western sides of the Red Sea.