The Southern birch mouse (Sicista subtilis) is a small-sized rodent species characteristic of the Palearctic steppes with westernmost occurrences in central Europe. The species was considered to be extinct in Transylvania (central Romania), but in our field survey we captured three living individuals near the city of Cluj-Napoca. On the basis of nuclear interphotoreceptor retinoid-binding protein and mitochondrial cytochrome c oxidase subunit 1 sequences, we assessed the taxonomic status of the newly found S. subtilis population by comparing them to available sequences, including the sequences of its subspecies. The Transylvanian samples were found to be genetically closest to the Hungarian samples of S. subtilis trizona. These new records extend the known geographic range of this rediscovered species and provide additional information on its habitat preference and external morphological features. Moreover, our phylogenetic tree reconstruction for seven Sicista taxa provides a basic insight into the phylogenetic relationships of the genus, placing the northern Eurasian taxa (S. betulina and S. subtilis) at the crown of the tree and the central Asian taxa at the base of the tree. The Transylvanian occurrence of S. subtilis trizona, which is endemic to the Carpathian Basin, is of high faunistic value as a result of an increase in the number of known populations of this subspecies -one of the most endangered rodents of Europe -from one to two.