Cellular context can be crucial when studying developmental processes as well as responses to environmental variation. Several different tools have been developed in recent years to isolate specific tissues or cell types. Laser-assisted microdissection (LAM) allows for the isolation of such specific tissue or single cell-types purely based on morphology and cytology. This has the advantage that (1) cell types that are rare can be isolated from heterogeneous tissue, (2) no marker line with cell type-specific expression needs to be established, and (3) the method can be applied to non-model species and species that are difficult to genetically transform. The rapid development of next-generation sequencing (NGS) approaches has greatly advanced the possibilities to perform molecular analyses in diverse organisms. However, there is a mismatch between currently available cell isolation tools and their applicability to non-model organisms. Therefore, LAM will become increasingly popular in the study of diverse agriculturally or ecologically relevant plant species. Here, we describe a protocol that has been successfully used for LAM to isolate either whole floral organs or even single cell types in plants, e.g., Arabidopsis thaliana, Boechera spp., or tomato.