A safe and sufficient supply of food is a national priority and is essential for the security and economy of the United States. Tools that have broad applications in monitoring genetic elements in agricultural systems, including prevailing or emerging soil-borne, food-borne and environmental pathogens, antimicrobial resistance elements, infectious diseases, and bioterrorism agents are vital in the development of a comprehensive safety and security program and in the future will define “first response”. Microarray is a high-throughput (10,000 to 30,000 gene targets per microchip), highly sensitive (detects as low as 0.2 copies/cell), and mature technology that has myriad biological applications. The applications include determination of gene profiles and function, assessment of organisms’ physiological state, identification of interacting proteins or pathways, genotyping, gene discovery and diagnostics. Community genomic analysis (CGA) is a microarray-based technology that can detect specific pathogens or genes in complex environmental samples that have numerous microbial agents, each varying in numbers and lineage. This technology provides a foundation for understanding prevalence, emergence, amplification and dissemination of specific genes in complex microenvironments including agricultural and animal biosystems. Following the development of the assay, extensive standardization and validation is required before incorporating the technology for use in agricultural systems. Validation protocols should include determining sensitivity and specificity of the assay, tandem-comparison to conventional protocols, as well as identifying sampling and sample-processing protocols, which may require a development of a template relevant to agricultural ecology. Development of a model(s) to analyze microarray data is vital to interpretation of results. Microarray is a powerful technology that has tremendous potential to generate scientific knowledge that is abundant in breadth and depth, and will contribute towards understanding of agricultural biosystems, microbial ecology and human-effects on these micro- and macro-environments to broad new frontiers.