Genetic diversity is one of three forms of biodiversity recognized by the IUCN as deserving conservation along with species and ecosystems. Seagrasses provide all three levels in one. This review addresses the latest advances in our understanding of seagrass population genetics and genomics within the wider context of ecology and conservation. Case studies are used from the most widely studied, northern hemisphere species Zostera marina, Z. noltii, Posidonia oceanica and Cytnodocea nodosa. We begin with an analysis of the factors that have shaped population structure across a range of spatial and temporal scales including basin-level phylogeography, landscape-scale connectivity studies, and finally, local-scale analyses at the meadow level-including the effects of diversity, clonality and mating system. Genetic diversity and clonal architecture of seagrass meadows differ within and among species at virtually all scales studied. Recent experimental studies that have manipulated seagrass genetic biodiversity indicate that genotypic diversity matters in an immediate ecological context, and enhances population growth, resistance and resilience to perturbation, with positive effects on abundance and diversity of the larger community. In terms of the longer term, evolutionary consequences of genetic/genotypic diversity in seagrass beds, our knowledge remains meagre. It is here that the new tools of ecogenomics will assist in unravelling the genetic basis for adaptation to both biotic and abiotic change. Gene expression studies will further assist in the assessment of physiological performance which may provide an early warning system under complex disturbance regimes that seagrasses are at or near their tolerance thresholds. At the most fundamental level, ecological interactions of seagrasses with their environment depends on the genetic architecture and response diversity underlying critical traits. Hence, given the rapid progress in data acquisition and analysis, we predict an increasing role of genetic and genomic tools for seagrass ecology and conservation. (C) 2007 Elsevier B.V. All rights reserved.