The practice of integrated management of plant diseases incorporates a vast body of scientific information for effective pathogen control as well as environmental stewardship. Pathogen biology, environmental and epidemiological patterns, preventative cultural practices and judicious chemical applications are a few examples of the scientific areas of research used to support integrated disease management. This body of work focuses on research involved in the integrated disease management approach: cover cropping, early detection of plant pathogens and a pathogen population study. The first chapter explores the effects of mixed-species cover crops on organic tomato crop productivity and disease severity in the field. This research, taken over three field seasons (2010, 2011 and 2012) at sixteen field sites in three states, Maryland, New York and Ohio (MD, NY and OH), each with distinct soilborne disease pressure, was based on measurement of plant growth and vigor, crop yield and disease ratings of naturally occurring infection over time. Our research revealed no short-term effects of cover crop treatments on productivity or disease severity in tomato crops. The second chapter looked at the same tomato crops, turning attention to how the cover crops affect fungal and oomycete pathogen presence in the rhizosphere of tomato plants. For this, two years (2010 and 2011) of field samples from 260 plots were evaluated using two molecular tools: macroarray analysis, a diagnostic tool used to test for the presence of 31 solanaceous pathogens, and terminal restriction fragment length polymorphism (T-RFLP), used to evaluate the microbial fingerprint of the samples. Our findings showed that cover crops did not affect pathogen presence in the rhizosphere and that macroarray was able to detect certain fungi with much greater sensitivity than T-RFLP. Chapter 3 explores the development of techniques used for early detection of Pseudoperonospora cubensis and P. humuli, causal agents of cucurbit and hop downy mildews, respectively. Two techniques were designed which allow for detection and differentiation of both pathogens from environmental samples: real-time PCR with locked-nucleic acid probes and high resolution melt curve analysis. These assays were then used to test for pathogen presence in air samples collected in New York using spore traps. Chapter 4 presents the results of a comparative analysis between RNA sequencing (RNA-seq) and genotyping by sequencing (GBS) conducted in order to determine which technique is most effective in single nucleotide polymorphism (SNP) identification for Pseudoperonospora cubensis and P. humuli, as well as to discover novel SNPs that determine population structure between and among these two genetically similar species. Finally, included in the appendix is a case study summarizing a collaboration with St. John's University in Tanzania, facilitated by a Horticulture Collaborative Research Support Program grant. The project aims were to train a graduate student in extension talks for IPM of tomato, implement the talks with growers and a pesticide alternative in an experiment-based field study.