Arbuscular mycorrhizal fungi establish one of the most successful endosymbioses with the vast majority of land plants, offering a range of benefits to their plant hosts. To gain insight in the molecular basis of this key interaction, numerous transcriptome studies have been performed on mycorrhized roots, especially in the model legume Medicago truncatula. However, because of the highly asynchronous nature of the mycorrhizal colonization process, more cell/stage‐specific insight is needed. Therefore, laser microdissection has been applied, which allows the contamination free dissection and collection of individual cells from any tissue. Subsequent expression profiling using GeneChip hybridization and more recently RNAseq approaches has started to give great detail in the transcriptome profiles of both host and fungus during different stages of the interaction. Here, I summarize the current application of laser microdissection (LMD) in arbuscular mycorrhiza research and highlight the role of several genes expressed at specific stages as revealed from genetic studies.