An effect of geographical barriers on the level of population structuring and ways of northwards colonization in the common shrew Sorex araneus was investigated by contrasting gene flow inferred by one Y-linked and eight autosomal microsatellites. A total of 102 shrews trapped at eight localities separated by mountain ridges of the Śnieżnik Massif (East Sudetes, Poland) were studied. The genetic structure of populations was estimated using the standard analysis of molecular variance based on F-statistic, as well as two clustering methods implemented in Structure and Geneland. In pair-wise population comparisons both FST and RST were estimated. A Mantel-test was used to investigate the patterns and causes of structuring. No significant correlation between genetic differentiation and geographical distance was found for autosomal loci and for the Y-linked locus. Significant genetic structuring was found in four out of six pairs of populations. Studying autosomal loci we found nonsignificant correlations between pair-wise matrices of FST and RST and the presence of the barrier. On the other hand, for the Y-linked locus these correlations were significant, both for FST and RST, suggesting reduced gene flow between populations for males. Patterns of genetic structuring in the common shrew of the Massif of Śnieżnik may suggest two possible ways of northwards colonization, which promoted genetic distinction of shrews migrating different routes.