The integration of classical ecological measurements with modern molecular and statistical analysis techniques is vital to a greater understanding of evolutionary relationships in time and space. Such understanding is the key to reassembling and rehabilitating diversity in the face of current environmental and climate changes. In this study, molecular markers were used to evaluate levels of genetic diversity and differentiation in sea sandwort (Honckenya peploides). Amplified fragment length polymorphism (AFLP) markers were applied to populations from the island of Surtsey and diversity measures were compared to selected populations from Heimaey, the south coast of Iceland, Greenland and Denmark. The current study indicates that: (i) Surtsey has the highest proportion of polymorphic markers as well as a comparatively high genetic diversity (55.5 PLP; 0.1974 HE) and Denmark the lowest (31.8 PLP; 0.132 HE), indicating an early stage of population establishment on Surtsey; (ii) the total genetic differentiation (FST) among Surtsey (0.0714) and Heimaey (0.055) populations was less than half of that found among the mainland populations in Iceland (0.1747), indicating significant gene flow on the islands; and (iii) positive and significant associations were detected between genetic differentiation and geographic distance (in km) at the broad scale.