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In contrast to many plant species, which had not survived in Central Europe during the last glacial maximum (LGM) and therefore recolonized from various southern or eastern refugia, we put forward the hypothesis that Juniperus communis L., a species with large ecological amplitude, could have survived in a cold steppe-like biome of the LGM throughout Central Europe. Fossils from locations above the 50th latitude dating back to 15 000—11 000 BP lead to this assumption. However, there is an absolute lack of records for the LGM. We used DNA markers to obtain genetic support for our hypothesis. If common juniper had survived in Central Europe and had not recolonized this area from diverse outside refugia, we would expect the gene pool of J. communis being imprinted in a different way than what is common for classic Holocene ‘recolonizers’. The latter tend to exhibit profound large-scale isolation-by-distance effects where genetic distances are positively correlated with geographic distances. Using AFLP (Amplified Fragment Length Polymorphism) markers in 23 modern common juniper populations sampled throughout Europe, we found a high level of genetic differentiation. However, there are no underlying phylogeographic signals or any other meaningful geographic genetic structures. Consistent with a scenario of perglacial survival there is no correlation between genetic and geographic distances as a result from Mantel tests.The present study again demonstrates the power of genetic tools when fossil records are not available. It contributes to an increasing knowledge about species distribution during unfavourable climatic conditions.