The endangered plant clay phacelia (Phacelia argillacea) is endemic to Spanish Fork Canyon, Utah, USA. In addition to habitat loss and abiotic stressors, herbivory is one of clay phacelia's major threats, but negative effects of herbivory have not been quantified. To examine the effects of simulated herbivory by small mammals, we grew 300 clay phacelia plants in a greenhouse (20 replicates of 15 half-sibling families). After six months of growth, half of the plants were randomly assigned to a defoliation treatment that mimicked herbivory from ground squirrels. After providing additional time for growth and natural pollination, we collected seeds and harvested shoots and roots from a subset of the plants. Among the 15 half-sibling families, we found significant genetic variation in shoot mass and a significant correlation between total mass when defoliated and undefoliated, suggesting a strong genetic component to growth. Defoliation significantly reduced seed production, shoot production and root production by 29%, 32%, and 35%, respectively. For these traits, interactions between family (F) and defoliation (D) were not statistically significant, suggesting fixation for tolerance to herbivory. In contrast, for root-to-shoot ratio, there was a statistically significant F × D interaction, revealing genetic variation for tolerance to herbivory. Depending on the type, intensity, and timing of herbivory, clay phacelia may benefit from either increased allocation to shoots or to roots. In fact, tolerance in terms of reproduction was correlated with shoot mass when defoliated, while tolerance in terms of growth was correlated with root mass when defoliated.