Colletotrichum trifolii is a fungal pathogen that causes anthracnose disease of alfalfa. We are studying the molecular regulation of prepenetration morphogenesis in C. trifolii to better understand disease development. Here we review the role of two conserved signaling molecules, Ras and cyclic AMP- dependent protein kinase, in fungal development. We also discuss the use of comparative biology and gene expression in heterologous systems to examine the function of fungal signaling proteins.