We studied the thermophilous grass Bromus erectus in Central Europe to determine its pattern of population genetic structure and genetic diversity, using ISSR-PCR fingerprinting to analyze 200 individuals from 37 populations. We found three genetic groups with a clear geographic structure, based on a Bayesian approach. The first group occurred west and south of the Alps, the second east and north of the Alps, and the third was formed by four genetically depauperated populations in Germany. The populations from Germany formed a subset of the Bohemian-Moravian populations, with one private allele. Two differentiation centers, one in the Atlantic- Mediterranean and the second in the Pannonian-Balkan area, were recognized by species distribution modeling. The geographic distribution of the genetic groups coincides with the syntaxonomic split of the Festuco-Brometea class into the Festucetalia valesiaceae and Brometalia erecti orders. We found a statistically significant decrease in mean ISSR bands per individual from south to north, and to a lesser extent from the east to west. The former was explained by Holocene long-distance migrations from southern refugia, the latter by the difference in the gradient of anthropopression. We hypothesize a cryptic northern shelter of the species in Central Europe in the putative Moravian-Bohemian refugium.