This study investigated the soil seed bank composition and standing vegetation over five different microhabitats (terraces, springs, wadi bed, saltmarshes and sand dunes) of a coastal ecosystem along the North Western Coast of Egypt. The floristic composition and diversity of the soil seed bank, as well as its similarity with the standing vegetation varied among wadi microhabitats. Such variation could be attributed to differences in disturbance intensity among microhabitats and variation of soil factors along the micro topographic gradient. Sand dunes showed the highest species richness and size of soil seed bank, followed by wadi bed and then terraces. Moreover, the diversity index of the seed bank and its similarity with standing vegetation were significantly greater in salt marshes, followed by the terraces and the lowest in wadi bed. The species richness of seed banks was increased in the sand dunes than the other ones. Annual/perennial ratio and species richness of the standing vegetation were high terraces in comparison with the other microhabitat.