Trees are extraordinary long living, sessile organisms that are faced quite variable environmental conditions and biotic stress factors during their life. They have a high level of genetic diversity to ensure adaptation and adaptability. With the massive advance in next generation DNA-sequencing, our abilities to screen this genetic variation have increased drastically. I will give an overview on the different genomic approaches, main target tree species and examples for application in the area of population genetics. Examples will show how high throughput SNP genotyping clarifies our views on taxonomy, phylogeography and provide us with useful data for different diagnostic applications such as species identification, tracking geographic origin and screening the level of pre-disposition to abiotic and biotic stress factors. Since a few years next generation sequencing and advanced molecular marker development have also been used in genetic association studies and transcriptome sequencing (RNASeq) in order to discover genes that are coding economical and ecological important phenotypic traits of trees. I will present examples on target phenotypic traits and the use in tree breeding programs