Macrophomina phaseolina (M. phaseolina) is a soil-borne fungal pathogen that causes charcoal rot disease in many plant species. This disease causes many problems to the soy industry as no consistently effective control is available. Using Medicago truncatula as a model, we study the molecular interactions between the pathogen and its plant host. In a previous study, microarray was used to determine expression of M. truncatula genes that were affected by the pathogen at different time points after infection. Data analysis showed that some auxin-related genes were differentially expressed. Auxin is a phytohormone required for normal growth and development and recent research is unveiling the molecular mechanisms of its role in plant defense. Based on gene expression profiling results, we hypothesize that M. phaseolina attacks its hosts by modulating auxin homeostasis. To test this hypothesis, we investigated if exogenous auxin application affected the susceptibility of the plant to M. phaseolina. The results demonstrated that the auxin imparted a slight resistance to the fungus indicating a potential infection strategy of M. phaseolina. To further identify genes that have potential roles in regulating auxin homeostasis and may be affected by M. phaseolina infection, we focused on the GH3 gene family in M. truncatula. GH3 genes encode enzymes that covert active hormones such as jasmonic acid and auxin into inactive amino acid conjugates. Expression of a GH3 gene was modulated by M. phaseolina infection according to microarray data. Using real-time quantitative PCR (RT-qPCR), we investigated the expression of 7 annotated GH3 genes in response to auxin or to M. phaseolina infection. We hope that better understanding of the molecular mechanisms involved in the infection process will help us to develop more effective management approaches and identify genes that could potentially be used to engineer disease-resistant plants in the future.