Tomatoes are a high value crop, but many diseases threaten optimal production and yield. In this dissertation three fungal and oomycete pathogens of tomato were examined using different genomic tools. In Chapter 1, the population structure and genetic diversity of the tomato leaf mold pathogen Passalora fulva were examined. High tunnel production of tomatoes is an important method of season extension and studies on P. fulva are necessary, as the disease appears more frequently. Races 0 and 2 were found to be the predominant races of isolates collected in the Northeast and Minnesota. A genotyping-by-sequencing (GBS) analysis found regional differentiation between the isolates collected in the Northeast compared to Minnesota. In Chapter 2, fungi from the genus Cladosporium were characterized. In early attempts to isolate P. fulva from leaves showing tomato leaf mold symptoms, more rapidly growing Cladosporium fungi were identified, yet they were not found to be pathogens of tomato in two high tunnel experiments. Phylogenetic, morphological, and GBS analysis offers additional characterization of the fungi. In Chapter 3, effector diversity within the US-23 clonal lineage of Phytophthora infestans, a devastating pathogen of tomato and potato that causes late blight, was examined. Previous work has demonstrated that some diversity exists within the US-23 clonal lineage. The PenSeq target enrichment sequencing tool enabled an examination of genes that are under selection. In the study of 12 isolates from the US-23 clonal lineage, variation in effector complement between isolates was identified. This is the first study focused on understanding differences in effectors within the US-23 clonal lineage and may lead to a better understanding of patterns of adaptive evolution that may exist within effectors present in isolates belonging to a single clonal lineage. Finally, in Chapter 4, early blight quantitative resistance in tomato was examined. Eleven tomato accessions with early blight resistance were sequenced to define cryptic introgressions underlying disease resistance in modern tomato (Solanum lycopersicum). Two quantitative trait loci (QTL) were fine-mapped on chromosomes 5 (EB-5) and 9 (EB-9), and predictions were made about genes within the QTL bounds. The 11 tomato accessions that were sequenced were compiled with 764 previously sequenced accessions to predict EB-9 resistance in several heirloom tomatoes, as well as accessions of S. lycopersicum var. cerasiforme and S. pimpinellifolium. Results were experimentally validated with mist chamber experiments.