Populations at different parts of the species range may vary in their population dynamics and in their genetic structure and variation. Geographically separated populations or those located at the edge of the range may differ from the populations located at the core, or even be independent of them. The peripheral populations may hold genetic variation that is important for the adaptive potential of the species and therefore be of special conservation value. We studied the distribution-wide population genetic structure of the Terek Sandpiper (Xenus cinereus) using 13 microsatellite loci and two mitochondrial DNA markers: the control region and cytochrome oxidase I (COI). We evaluated the difference in genetic variation between the peripheral and core populations. Specifically, we sought signs of changes in population sizes and evaluated the management need of the populations. Distribution-wide differentiation was negligible, but geographically isolated populations in Finland and Dnieper River basin in Eastern Europe were differentiated from the main range. Edge populations had lower genetic variation than populations at the core when estimated with microsatellites and the COI, supporting the hypotheses where the core area of the distribution preserves the most variation. However, no such trend was observed with the control region data, which follows the model of no change throughout the distribution. The differences between the markers may reflect their different mutation rates, or be linked to the species’ dispersal behaviour. Our results revealed low overall nucleotide diversity and signs of past population contractions followed by expansion. Although the estimated current effective population size is large and therefore global conservation measures are not needed, the Finnish and Dnieper River basin populations nevertheless warrant management actions – not only because they may possess variation not present anywhere else, but also due to their smallness and large distances to the main range.