Switchgrass (Panicum virgatum L.), a perennial C4 biomass crop native to North America, suffers from a reduction in germination due to Bipolaris seed rot (BSR) and yield reduction from Bipolaris leaf spot (BLS), both caused by a necrotrophic ascomycete fungus named Bipolaris oryzae (Breda de Haan) Shoemaker. To manage the diseases under economically competitive conditions, breeding switchgrass for resistance and silicon amendment were two potential approaches. Screening methods in a greenhouse were established for BSR in seeds and BLS in 4-week-old seedlings. Half-sib progenies were used to estimate narrow-sense heritability of resistance to the two diseases. Moderate heritability estimates of resistance to BSR suggested successful gain from selection, whereas non-significant heritability of resistance to BLS suggested no progress from selection. Such heritabilities accurately predicted the result from two cycles of recurrent phenotypic selection in ‘Cave-in-Rock’ and ‘Shelter’. The progress of resistance to BSR was more than 50% cycle-1 in both cultivars whereas the progress of resistance to BLS was not significant. Such difference between resistances to BSR and BLS resulted in no correlation between the disease resistances. To dissect the resistance to BLS, genome-wide association was conducted in the Northern Association Panel. The BLS evaluation was conducted in 479 mature switchgrass plants via field evaluation, detached leaf assay, and leaf disk assay. Multi-trait Genome-wide association studies (GWAS) from different phenotype combinations in four subgroups revealed potential resistance genes associated with 18 markers on chromosomes 1b, 2a, 2b, 3a, 3b, 5a, 5b, 6a, 7a, 8a, 9a, and 9b explaining phenotypic variances of 6.32 to 26.72%. Within linkage disequilibrium of 20 kb, there are some potential resistance genes including genes encoding Myb, cytochrome P450, isocitrate lyase, E3 ubiquitin-protein, etc. These markers can be used in genomics-assisted breeding in the future. Besides breeding, silicon amendment has also explored the potential based on the effectiveness against BLS in rice. However, for switchgrass in a greenhouse, silicon amendment (either incorporated into the potting mix or foliar drenches) showed no significant effect BSR and BLS, suggesting more studies are needed on field application and long-term effects of silicon.