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The brown bear (Ursus arctos) population in Estonia is a part of the large fragmented Eurasian population, constituting a piece of its northwesternmost branch. The large forested region in northeastern Estonia has been a core area for bears since the Holocene. Although half of the country is covered by forest, suitable habitats for bears are limited. Extensive forest clearance and human disturbance are major threats to Estonia's brown bear population. Counting and measuring of bear tracks have been used to monitor bear population in Estonia, resulting in a minimum estimate of 231 brown bears in 1998. Estimates based on reports from hunting organizations produced a number close to 600. However, a methodology has yet to be developed that will yield reliable numbers. We are currently testing non-invasive sample collection methods, genetic identification, and mark-recapture models to analyze brown bear population size, density, and genetic variability.