Advances in genetic engineering make it possible to improve or introduce desired traits in crops at an accelerating pace. In Switzerland, the import of genetically modified (GM) crops are tightly regulated. A core mandate of federal authorities is to ensure effective monitoring. GM crops of the past decade contained simple, well characterized modifications that can be efficiently recognized by currently implemented screenings. Newer GM technologies (i.e. CRISPR variants) are used to create more precise and more complex modifications. This creates an urgent need for validated tools that allow the precise identification of genome editing in imported crops. In this research project, we accomplished the following aims. We first designed and validated a next-generation multiplex sequencing assay targeting GM loci monitored in Switzerland and the EU. The assay was capable to identify the species from which the material originated, show reasonable sensitivity despite multiplexing hundreds of loci simultaneously. In the next set of aims, we developed a mathematical model that lays the foundation to detect cis-genesis gene editing events in plant or animal specimen. We then wrote software to apply the mathematical model to genome sequencing data and, finally, we analyze rice genome sequencing datasets to assess the sensitivity and performance of the software. In summary, we built foundations how future challenges of GM monitoring can be addressed.