Cyanobacterial symbioses of land plants have evolved multiple times independently. But only in the water fern Azolla the cyanobiont is inherited. The symbiosis rests on a singular event about 60 million years ago. The life cycles of both fern and cyanobiont are tightly co-ordinated and in natural habitats neither is able to survive alone. This requires well-coordinated communication. We are interested in the mechanisms that allow for this interaction and the genomic consequences that result from it. Using RNASeq, untargeted metabolomics and image analyses after compound treatment we have identified phenolic compounds produced by Azolla that impacted in particular motility of symbiotic cyanobacteria. Modulating motility is key to initiate cyanobacterial symbioses and in Azolla it is the central step to ensure vegetative and sexual inheritance for 60 million years. We currently profile a fine-grained gradient of the symbiotic development in Azolla and its cyanobiont. With this we capture the major functional symbiotic transition during vegetative inheritance and found the first molecular evidence of active induction of motility in the cyanobiont. For further considering the complexity of the symbiotic interaction at the site of functional exchange, we explore the associated microbiome and its impact on the symbiotic interaction.