Projects in ecology and environmental research have long been supported by population and molecular genetic analyses. In recent years, technical and bioinformatic developments have created the conditions for carrying out these analyses cost-effectively and thus making them available for many research projects. Two examples from the Keylab Genome Analytics & Bioinformatics will be used to present how high-throughput sequencing methods on the Illumina and Oxford Nanopore platforms are used to a) perform population genetic analyses based on SNP polymorphisms and b) create the basis for differential gene expression analyses in non-model organisms.