Research on different endophyte taxa and the related scientific disciplines have largely developed separately, and comprehensive community-level studies on bacterial and fungal interactions and their importance are lacking. Here, we discuss the transmission modes of bacteria and fungi and the nature of their interactions in the endosphere at both the molecular and physiological level. Mixed-community biofilms in the endosphere may have a role in protecting endophytes against encountered stresses, such as from plant defense systems. However, transmission from static (in biofilms) to free-living (planktonic) forms may be crucial for the exploration of new habitable spaces in plants. Important features previously recognized as plant-microbe interactions or antagonism in endophyte genomes and metagenomes are proposed to have essential roles in the modulation of endophyte communities.