The Eurasian otter (Lutra lutra) is currently listed as Near Threatened (NT) according to IUCN. Recent increases in numbers of otter in Sweden have been documented, yet population size and health is still currently unknown. In this study, we aim to develop a panel of SNP markers that are highly informative for individual identification and can therefore be used regularly to monitor the populations using non-invasive sampling methods. To achieve this, we will sequence a reduced representation of the genomes (RADseq) of 94 individuals spanning Fennoscandia. The sequence data will be analysed for SNPs, which will be stringently filtered down to 192 highly informative SNPs for individual identification. It will be this panel that will be used for monitoring the Swedish population of otters. The RADseq sequence data will additionally be used to characterize the current state of the otter population across Fennoscandia. We aim to assess demographic history, levels of inbreeding, population structure, and other types of analyses. Through this work, we will be able to monitor the otter population in Sweden with the panel of SNPs, as well as provide an overview of the population health of otters throughout Fennoscandia.