Dynamic mechanical thermal analysis (DMTA) on individual native silk fibers demonstrates changes in the dynamic mechanical properties of storage modulus and loss tangent as a function of temperature and temperature history ranging from -100 to 250 °C. These property changes are linked quantitatively to two main types of change in the silk structure. First, the evaporation of water with increasing temperature up to 100 °C increases the storage modulus and removes two characteristic loss tangent peaks at -60 and +60 °C. Second, various discrete loss tangent peaks in the range 150-220 °C are associated with specific disordered silk structures that are removed or converted to a limiting high-temperature relaxed structure by the combination of increasing temperature and static load in the DMTA tests. The results identify important origins of silk filament quality based on the analysis of measurements that can be traced back to differences in production and processing history.