Mountain ecosystems are hotspots of biodiversity distribution and conservation. Mountain landscape genetics is an important branch of the subject Landscape Genetics, which studies the genetic patterns of wild populations, their underlining mechanisms and influencing factors at the mountain landscape scale. Mountain landscape genetics research is of great significance for in-depth understanding of the formation of species’ spatial genetic structure, speciation and differentiation mechanism, and can provide important guidance for the effective conservation and management of rare and endangered species and mountain biodiversity. To better understand the development trend and key research issues in the field of mountain landscape genetics, and to provide scientific reference for protection and management of biodiversity and mountain ecosystems in the future, we systematically reviewed relevant studies retrieved from the core database of Web of Science and China National Knowledge Infrastructure (CNKI). A total of 192 English and 31 Chinese literatures in the field of mountain landscape genetics published from 1999 to 2020 were summarized and analyzed. The results showed that the field has been developing rapidly since 2008, with numerous research institutions from 46 nations involved in these published studies. The geographical research hotspots included the Rockies, Sierra Nevada, and Appalachians in North America, the Alps and Pyrenees in Europe, and the Himalaya-Hengduan Mountains in Asia. The studied taxa included fungi, plants, arthropods and vertebrates, where vertebrates were the most studied taxon accounting for 62.0% of the total number of published English articles. Among the vertebrates, mammals (accounting for 52.9% the total number of vertebrate articles) and amphibians (23.5%) were the most studied taxa. Current research directions of mountain landscape genetics mainly include: (1) identifying paths or barriers of gene flow in the mountain landscapes; and (2) quantifying the effects of mountain landscape characteristics on the temporal and spatial variations of population genetic structure. Of all Asian countries, China has published the largest number of articles on mountain landscape genetics. Research on mountain landscape genetics in China has been rapidly advancing in the past decade, with plants (accounting for 62.3% the total number of Chinese studies) and vertebrates (35.8%) being the focal taxa. The largest number of vertebrate studies were conducted on amphibians (accounting for 52.6% the total number of vertebrate publications). Himalayas and Qinling Mountains were the focal mountainous regions in China. In this review, we also provide suggestions about the gaps existing in mountain landscape genetics and the key research issues to be addressed for current and future studies.