Recognising patterns of genetic diversity and connectivity is integral to understanding the mechanisms behind population declines and formulating management plans for the conservation of threatened or endangered species. This is particularly important for clonal organisms such as seagrasses, which are experiencing rapid global decline. This study quantifies genetic diversity within 12 naturally fragmented Posidonia australis meadows on the east coast of Australia, using a set of eight microsatellite DNA markers. Genetic diversity increased with latitude, moving away from the range-edge, and was significantly lower in six mid-range endangered meadows and the two northernmost meadows. These meadows also showed evidence of shared multilocus genotypes despite significant geographic separation. The four southernmost meadows were genetically differentiated from all other meadows further north, and all multilocus genotypes identified were unique to their sample locations. We conclude that patterns of low diversity in the endangered and northern meadows are likely due to a population bottleneck caused by a range-edge effect. A common ancestral source meadow existing prior to historical sea level changes may explain the sharing of multilocus genotypes, as contemporary gene flow between these geographically isolated meadows is unlikely. Our findings have important implications for conservation, highlighting the endangered and range-edge populations as those potentially most at risk of extinction should environmental conditions change. These results can be utilised for the location of suitable donor populations for transplanting purposes as a means of mitigating further declines. © 2014 Springer Science+Business Media Dordrecht.