The phytosphere is an attractive habitat for microorganisms due to an abundance of nutrients and relative environmental stability. The microorganisms that occupy this habitat assist in the uptake of nutrients from soils and can exert considerable influence upon the overall health of the plant. Recent technical advances in environmental microbiology have enabled the tracing and assessment of these microorganisms using rapid and simple molecular techniques without any culture-dependent bias. We herein review the current status of these modern molecular techniques in the study of plant-associated microbes, and summarize the issues relevant to the phytosphere from the aspect of both basic and applied science.