During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today's continuum of associations ranging from parasitism to mutualism. Through phylogenetics, cell biology and reverse genetics extending beyond flowering plants into Bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms employed in non-flowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen resilient crops.