Leaf cutting ants are member of a multitrophic system. They are cultivating the garden fungus Leucoagaricus gongylophorus, which serves them as major food source. This mutualistic symbiosis is threatened by several pathogens. The ants are therefore defending their colony by removing any suspicious material from the fungus garden into waste chambers and additionally by using chemical arms. Beside their own antimicrobial metabolites, symbiotic Actinomyces are supporting this survival conflict with their antibiotics. It became evident, that complex microbial communities are part of the whole live style of leaf cutting ants. Beside their mutualistic role, the involved microorganisms pursue selfish interests by using secondary metabolites to hinder other competing symbionts of the leaf cutting ants. A new method to easily identify microbial chemicals involved in leaf cutting ants’ ecosystems has been established. Antimycins, actinomycins and valinomycins were identified. The potential of some of these antibiotics to shape the complex microbial communities present in the ants’ nest has been tested. Beside pathogens also Actinomyces-symbionts and the garden fungus were inhibited. For the first time it was possible to directly detect known antibiotics in the waste material and on the cuticle of Acromyrmex ants. A plasmid for future investigations on the uptake of Actinomyces by leaf cutting ants has been constructed. Feeding studies with labeled compounds helped to investigate the biosynthesis of the 3-aminosalicylic acid-unit of the antimycins which apparently involves a shift of the carboxyl group of the anthranilic acid. Additionally it was shown that the antimycins already decompose under weak alkaline conditions, generating γ-butyrolactones.