Macrophomina phaseolina is a soil-borne fungal pathogen that causes the charcoal rot disease in many plant species. This disease causes many problems to the soy industry as no consistently effective control has been found. Using Medicago as a model, we study the molecular interactions between the pathogen and its plant host. A microarray chip was used to measure the changes in the expression levels of M. truncatula genes when the plant was under attack by the pathogen at the 24-hour, 36-hour and 48-hour intervals. Analysis of the data showed that genes in the auxin transport and response pathways were differentially expressed. Auxin is a phytohormone that is commonly associated with plant growth, but recent discoveries have turned up a possible link between auxin and plant defense. We will be testing the effect of auxin on the plant's response to M. phaseolina. With the results obtained, we hope to better understand the molecular interactions between the pathogen and its host, which can then allow us to determine how best to control this disease biologically.