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Loss of genetic variation from genetic drift during population bottlenecks has been shown for many species. Red deer (Cervus elaphus) may have been exposed to bottlenecks due to founder events during postglacial colonisation in the early Holocene and during known population reductions in the eighteenth and nineteenth centuries. In this study, we assess loss of genetic variation in Scandinavian red deer due to potential bottlenecks by comparing microsatellite (n=14) and mitochondrial DNA variation in the Norwegian and Swedish populations with the Scottish, Lithuanian and Hungarian populations. Bottlenecks are also assessed from the M ratio of populations, heterozygosity excess and from hierarchical Bayesian analyses of their demographic history. Strong genetic drift and differentiation was identified in both Scandinavian populations. Microsatellite variation was lower in both Scandinavian populations compared with the other European populations and mitochondrial DNA variation was especially low in the Swedish population where only one unique haplotype was observed. Loss of microsatellite alleles was demonstrated by low M ratios in all populations except the Hungarian. M ratios' were especially low in the Scandinavian populations, indicating additional or more severe bottlenecks. Heterozygosity excess compared with the expectation from the number of observed microsatellite alleles suggested a recent bottleneck of low severity in the Norwegian population. Hierarchical Bayesian coalescent analyses consistently yielded estimates of a large ancestral and a small current population size in all investigated European populations and suggested the onset of population decline to be between 5,000 and 10,000 years ago, which coincide well with postglacial colonisation. [ABSTRACT FROM AUTHOR]