The application of time and cost efficient high-throughput sequencing technologies called NGS, nextgeneration sequencing enables researchers to tackle completely new problems in medicine as well as in agriculture. The availability of increasing genetics data from various species along with the use of new molecular biology and bioinformatics methods for data handling shifts the focus from single genes or gene products to the understanding of reactions, interactions and entire biological systems. In weed research the application of these methods is straightforward. The analysis of the genome and transcriptome of a weed can, for instance, lead to the identification of suitable gene products as target-sites for herbicides. Gene expression analyses result in a deeper understanding of herbicide resistance (target-site as well as non target-site resistance). In addition, sequencing the metagenome provides insights into potential interactions with microorganisms in the habitat of interest.