Development of DNA markers in forest genetics has overcome the limitations on the number of the used to date morphological and biochemical markers and provided the tools that study variation in coding, non-coding and highly variable regions of both nuclear and organelle (chloroplast and mitochondrial) genomes. In phylogeografic and phylogenetic studies of tree populations as well as gene flow, organelle genomes and highly variable genetic markers proved to be highly informative. Many genetic markers belong to so-called anonymous DNA marker type. Techniques based on these markers are: microsatellites or simple sequence repeats (SSRs), restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), and amplified fragment length polymorphisms (AFLPs). These marker types generally measure neutral DNA variation. They proved to be very useful (with different efficiency) in the analyses of phylogenetic relationships, population structure, mating system, gene flow, parental assignment, introgressive hybridization, marker-aided selection and genetic linkage. However, anonymous-DNA markers are not useful for measuring adaptive genetic diversity where newly developed marker system named expressed sequence tag polymorphisms (ESTPs) could lead to further progress. The need of implementation of those DNA based, powerful, new and highly informative methods in forest genetic research have arisen recently concerning high interest in genetic variability and fingerprinting of poplar species.