Endophytic fungi have a very specific mutualistic relationship with their hosts. The beneficial effects are bestowed to the host by way of metabolites called alkaloids. This research is of interest because while helping the plant increase drought tolerance and pest resistance, it also has been known to cause toxicosis and staggers in cattle, costing the cattle industry millions. Several assays were performed to understand the genetics and secondary metabolites of endophytes in five Festuca and five Lolium samples. To identify the endophytes, they were first isolated from the host and grown on potato dextrose agar (PDA). The isolates were identified through amplification and sequencing of their rDNA genes. Universal primers were created to amplify the genes and ITS regions. The PCR products were cloned and sequenced and sample sequences were compared to the known sequences recorded in GenBank. The endophytes were from the genus Neotyphodium. A cladogram to determine the similarity of the isolates was based upon 238 markers from AFLPs. There were several distinct groupings of endophytes depending upon their respective host. With the exception of a couple isolates, the samples from Festuca and Lolium grouped into their own respective clades. The differing fungal colonies were distinct enough to not be associated with the other clades. Secondary metabolites (alkaloids) were identified and quantified by extracting the alkaloids in planta, and then running the samples through the GC with internal standards. Loline was the major alkaloid detected.