The present study conducted to assess the relationship between vegetation and soil seed bank at protected versus unprotected sites at coastal habitats in Libya, where two sites (protected and non-protected) were selected and soil seeds estimated manually by sieving and flotation method. The results revealed that 190 species recorded in the protected site for both vegetation and soil seed bank, among them 87 perennials, 2 biennials and 101 annual and included 126 genera belonging to 34 families. While the non-protected site vegetation attained 104 species, among them 51 perennials, 2 biennials and 51 annuals and 82 species in soil seed bank, from which 12 species were found only as seeds and 77 species were found as seeds and as vegetation, but 22 species were found only as vegetative forms. The life form spectrum was dominated by therophytes which represented by 106 species, (55.78%) of the total number of recorded species, hemicryptophytes 32 species, (16.84%), cryptophytes 23 species, (12.1%), Chamaephytes 16 species, (8.4%) and phanerophytes 12 species, (6.3%). Soil seed bank increased with the increases of soil salinity, soil organic matter content, calcium carbonates and sandy textured soil. The higher similarity index between the vegetation and soil seed bank recorded in the protected site (100 %), while the lower one detected in non-protected site (75.26%). Vegetation protection may lead to formation of a huge storage of seeds in soil more than in the non-protected vegetation. Accordingly, soil seed banks can provide a clear picture about the present , as well as the past vegetation and could be play a vital role in conservation and restoration of rare and endangered species after the disturbance processes in the coastal habitats