The Carpathians are a range of mountains forming an arc roughly 1,500 km long across Central and Eastern Europe. They are an important area for biodiversity and belong to one of the major refuges of the last ice ages for many organisms. The forests of the Carpathians are dominated by spruce, which have suffered continuous outbreaks of the eight spined spruce bark beetle, Ips typographus, in recent decades. The phylogeography of this spruce pest is well documented, however, little is known on small scale, i.e., the Carpathians. Here we applied a mitochondrial marker and studied the genetic variation and structure of Carpathian populations and compared data with published one from other European populations. Twelve haplotypes were characterized and 42 % of those were not detected in other European populations. Despite a slight genetic structure, differences were observed in the haplotype distribution and diversity between the Western/Southern Carpathians and the Eastern Carpathians reflecting at least two potential refugial areas for I. typographus within the Carpathian mountain system. Further data show that the Eastern Beskidian Mountains of the Carpathians could act as barrier for several European haplotypes. This small-scale analysis reveals that the Carpathians have been an important glacial and post-glacial refuge for I. typographus. This information is important for a preventive and reactive forest management.