Plants provide multiple habitats for microbial life. Their roots recruit microorganisms to the surrounding soil, or rhizosphere, by exuding carbon compounds. Above ground, in the phyllosphere, their photosynthesizing tissues are colonized by a subset of microbes from the rhizosphere as well as those deposited by the the surrounding air and rainfall. While many microbes live as epiphytes on the surface of plant tissues, others reside within host tissues as endophytes. Endophytic microbes can benefit the host or be agents of disease. Regardless of whether they help or harm, these microorganisms can influence the growth and nutrient cycling of their plant hosts and are therefore variables of interest in both agricultural and ecological studies. While a great deal of foundational work has characterized the collections of microbes inhabiting plant tissues around the world, a synthesis with principles of community ecology is now required in order to understand how these plant microbiomes assemble. With a better understanding of how microbiomes form, we hope to learn how to cultivate or engineer plants to recruit microbial partners that can enhance growth or deter pathogens. This dissertation addresses basic questions about microbiome assembly in plants-- the same questions that ecologists seek to answer about how microbial communities form in the soil, on our skin, and in our guts. Namely, How do host and environmental factors lead to habitat filtering in the microbiome?How repeatable is the process of microbiome assembly? How do interactions among microbes shape the microbiome over time? How can we find the host genes that shape the microbiome? How does microbiome assembly change across host generations? To address these questions, I present results from descriptive studies on the native microbiome of the model plant species Arabidopsis thaliana in the midwestern United States as well as controlled experiments using isolates of its Pseudomonas pathogens from that environment.