Even though the phylogeography of hedgehogs has been well studied, information on the genetic variability of the northern white-breasted hedgehog Erinaceus roumanicus from the Balkans is lacking, since the previous studies were based on very limited sampling across the Balkans. The aim of this study is to estimate the genetic diversity and population structuring of E. roumanicus from the Central Balkans and to complement an already proposed phylogeographic scenario of this species. Tissue samples of 108 road-killed northern white-breasted hedgehogs were collected across the Central Balkan countries of Serbia, Montenegro, Bosnia and Herzegovina, and Macedonia. A partial fragment of the mtDNA control region (CR) was amplified and sequenced. Nine of 13 haplotypes detected in this study have not been previously published. The results indicate a moderate level of haplotype diversity of E. roumanicus from the Central Balkans and differentiation into four spatial groups, which are named after the approximate sampling localities as northwestern-central, northeastern, southwestern, and southeastern groups. The observed population structure in the Central Balkans remains less pronounced in further phylogenetic and phylogeographic analyses of the dataset comprising E. roumanicus and E. concolor mtDNA CR sequences. The central position of Balkan haplotypes in a median-joining network indicated its role as a primary source population for postglacial northward expansion.