The South Bay subspecies of the salt marsh harvest mouse is endemic to the tidal marshes and associated transition zones of the South San Francisco Bay.   Habitat for the species was eliminated and fragmented by the diking of tidal marshes and to create salt ponds and developed areas.  We describe the remaining habitat for the species and the existing barriers to movement between what are now isolated populations.  This species is cover-dependent and unlikely to move long distances over bare ground.  Remaining habitat is largely in the form of narrow strip marshes on the outboard side of salt pond levees, which are habitats further threatened by sea-level rise.  One of the major components of the restoration plan for the South Bay Salt Pond Restoration Project was to restore these lost tidal marshes and to reconnect these isolated populations.  The restoration of the South Bay marshes will be most beneficial to the salt marsh harvest mouse if it includes the creation of complete marshes, i.e. marshes with all zones (i.e. cordgrass, pickleweed, peripheral halophytes, and upland vegetation) and hence provide plentiful escape cover from tidal inundation.  Connectivity between these marshes is also critical.  Aspects of the restoration plan are discussed, and the influence of the ecology of this species on the planning process and eventual restoration are detailed.  The evolution of restored tidal marshes based upon models of sediment deposition and vegetation colonization are described.  Methods to accelerate the process of restoration for the species are discussed, as are proposed measures to enhance high tide escape zones.