Abstract <p>Molecular genetic markers (MGMs) are powerful tools that allow researchers to study the population structure, assess the level of genetic variability, track migration processes within the species. The review considers various aspects and effectiveness of using various MGMs for studying the genetic diversity of different conifer species. It provides an analysis of history of MGM development, their classification and characteristics, and examples of MGMs most frequently used in studies of conifer species. Particular attention is given to modern DNA markers developed using next-generation sequencing (NGS) technologies. Genome-wide association studies (GWAS) of important adaptive and breeding-valuable traits across a large number of conifer genes became possible only due to such modern DNA markers. Compared with traditional markers, they provide more comprehensive information on genetic variation in conifer species, allowing researchers to identify associations of genetic variation with variation in such important traits as disease resistance, drought tolerance, growth rate, wood quality, etc., as well as with variation in environmental factors and bioclimatic parameters. It should be noted that in general, the topic of MGMs is vast and covers thousands of publications. Therefore, the development and use of MGMs in the studies on conifers, one of the most important plant groups, is the primary focus of this review. Moreover, the main focus will be on publications on conifers growing in Russia that, in our opinion, still remain insufficiently studied genetically. Therefore, the authors apologize in advance to all researchers, whose worthy publications were not mentioned in this review due to limitations of its permissible volume.</p>