The production of antimicrobial peptides (AMPs) in response to invading pathogenic microbes is an effective and ancient innate immune strategy which is conserved in all analyzed present-day eukaryotes. However, organisms are not only threatened by microbes but on the contrary, they often form beneficial symbiotic associations with them. There is a growing number of reported cases, both in animals and plants, which demonstrate the critical involvement of AMPs also in these symbiotic interactions. Notably, AMPs can intervene in the selection and maintenance of symbiotic microbial communities.