This study assesses the genetic structure and gene flow of the salt marsh species Salicornia tegetaria between estuaries and tests three hypotheses: (1) that the relocation of estuaries on a shallow continental shelf during the last glacial maximum created a historical biogeographic barrier, the exact location of which we attempt to pin-point, (2) that there is connectivity and thus gene flow at present between estuaries, and (3) that some estuaries have higher genetic diversity and are therefore of higher conservation priority. DNA samples were collected from 17 estuaries and used to create haplotype networks. Analyses of molecular variance, isolation by distance, selective neutrality and genetic distance between estuaries were also conducted. Eleven ITS ribotypes, one found exclusively between Olifants and Breede Estuaries, and eight rpS16 haplotypes were recovered with a dominant haplotype occurring in most estuaries. The remaining ribotypes and haplotypes from ITS and rpS16 sequences were unique, predominantly on the South and East Coast. A high amount of gene flow and an increase in genetic differentiation from west to east was found. The topography of the continental shelf and diverging ocean currents did provide a historical geographic barrier during the last glacial maximum approximately 18,000 years ago. A high degree of connectivity between estuaries allows for the exchange of genetic material in the direction of the ocean current, but long distance dispersal is also suggested. Repeated habitat fragmentation, most likely due to fluctuating sea levels, contributed to a higher amount of rare haplotypes on the South and East Coast. This study provides baseline information on a salt marsh species for which there is a paucity of data that is widely distributed in an ecosystem that is likely to be heavily impacted by climate change. Keywords: Chloroplast DNA, Glasswort, Nuclear DNA, rpS16ITS, Salt marsh, Samphire, Sea level.