The Nordic countries have a special responsibility to ensure long-term survival of the domestic and the remaining native wild reindeer herds. Both are exposed to a combined natural and human induced selection influencing phenotypic characters which vary between and within the different management regimes. Knowledge of how phenotypic characters respond to various selection regimes are crucial for predicting their response to future environmental changes. Indeed, this is critical for assessing the breeding scheme practised in reindeer husbandry and the feasibility of applying new selection techniques emerging. The present increased habitat modification and climate change, urge to study the effects of past and present evolutionary changes on intraspecific genetic diversity to decipher the evolutionary consequences of various environmental changes. Examining contemporary and previous genetic structure of Fennoscandia reindeer provides a unique opportunity to assess the effects of historical processes including human interference, and the impact of climate on gene flow and genetic diversity.