Locoweeds are Astragalus and Oxytropis species that contain the toxic alkaloid swainsonine. Swainsonine accumulates in all parts of the plant with the highest concentrations found in the above ground parts. A fungal endophyte, Undifilum oxytropis, found in locoweed plant species, is responsible for the synthesis of swainsonine. By using quantitative PCR, the endophyte can be quantified in locoweed species. Endophyte amounts differ between plant parts and in some instances do not mirror the concentrations of swainsonine in the corresponding parts. Two groups of Oxytropis sericea were identified: one that accumulated high concentrations of swainsonine and another where swainsonine was not detected, or concentrations were near the detection threshold. The plants with high swainsonine concentrations had quantitatively higher amounts of endophyte. Alternatively, plants with low or no swainsonine detected had quantitatively lower endophyte amounts. In addition, swainsonine and endophyte concentrations were not distributed uniformly within the same plant when separated into stalks (leaves, scape(s), and flowers/pods). These findings provide evidence as to why plants in the same population accumulate different concentrations of swainsonine, and they have important implications for sampling of locoweed plants.