The plant microbiome is a source of relevant information for enhancing plant health. To characterize the plant microbial community, several steps are necessary, including experimental design, sample preparation, nucleic acid extraction, and sequencing and data analysis. The plant microbiome may vary across different plant organs and tissues, and molecular characterization of the microbiome commonly involves amplicons of phylogenetically informative marker genes. Hence, considering the relevance of genomic DNA for understanding the plant microbiome, the aim of this chapter is to provide fundamental knowledge for researchers and their teams to perform the separation of genomic DNA protocol through agarose gel electrophoresis.