Several boreal taxa can be found in southern latitudes in fragments of high altitude alpine habitat. Some of these taxa have remained isolated from the main populations in northern latitudes as a result of the distribution changes during the last glaciations, being known as glacial relict populations. Such relict populations have often differentiated from the main population as a result of isolation and genetic drift. The Tengmalm's owl Aegolius funereus is a widespread boreal forest species distributed throughout boreal Eurasia and North America. The westernmost Eurasian breeding population is located in the Pyrenees Mountains, and was discovered less than 50 years ago. We studied the genetic structure of this Pyrenean population of Tengmalm's owl, and compared it with a northern latitude population from Fennoscandia. Despite being isolated by several hundred kilometres from the closest breeding grounds, we found no differences in the genetic structure of the mitochondrial DNA when compared with the central population. Our results suggest that this population has been recently, or still is connected with the main population.