Semi-domestic reindeer play a vital role in the culture and livelihoods of indigenous people across the northern Eurasia. These animals are well adapted to harsh environmental conditions, such as extreme cold, limited feed availability and long migration distances. Therefore, understanding the genomics of reindeer is crucial for improving their management, conservation, and utilization. Here we have generated a new genome assembly for the Fennoscandian semi-domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilized to explore genetic diversity, population structure and selective sweeps in Eurasian R. tarandus populations which was based on the largest populations genomics dataset for reindeer, encompassing 58 individuals from diverse populations. Phylogenetic analyses revealed distinct gene clusters, with the Finnish Forest reindeer standing out as a unique sub-species. Divergence time estimates suggested a separation of ~52,000 years ago between Northern-European R. t. fennicus and R. t. tarandus. Our study identified three main genetic clusters: Euro-Beringian, South/Central European and the Finnish Forest reindeer. Furthermore, two independent reindeer domestication events were inferred in Fennoscandian and Russian semi-domestic reindeer. Notably, shared genes under selection, including retroviral genes, point towards molecular domestication processes that aided adaptation of this species to diverse environments.