Exotic plant invasions represent a threat to natural and conserved ecosystems. In this study, the effect of the invasive exotic Acacia saligna on native floristic diversity was evaluated at Zaranik and Ahrash Protectorates that representing arid and semi-arid climate, respectively along the Mediterranean dunes of Sinai. At each site, 35 plots were randomly established. The community attributes of native species including species number, species richness, species evenness and dominance–diversity curves were measured and compared between invaded and uninvaded patches. Results showed that all the measured community attributes were significantly lower in the invaded than uninvaded patches at both sites. In addition, the dominance–diversity curves indicated that invaded patches had less species richness with monospecific communities. Furthermore, the effect of A. saligna on the native flora is dependent on its canopy size and the aridity. Larger canopy at the arid site has negatively greater impact on the diversity of native species. The vitality survey showed that the leaf litter accumulation of A. saligna has a detrimental effect on the health of the native dominant Artemisia monosperma shrubs in the adjacent uninvaded patches. Markedly, the present study indicates that A. saligna has a potential threat to the native plant diversity within the two Mediterranean conservation protectorates. Restoration options to reduce exotic A. saligna plants in the North Sinai sand dunes were found to be the introduction and management of native sand trapping plant species.