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The South Atlantic Anomaly (SAA) is a region at Earth’s surface where the intensity of the magnetic field is particularly low. Accurate characterization of the SAA is important for both fundamental understanding of core dynamics and the geodynamo as well as societal issues such as the erosion of instruments at surface observatories and onboard spacecrafts. Previous studies applied crude measures of the SAA. Here we propose new measures to better characterize the SAA area and center, accounting for global dipole changes and shape anisotropy. Applying our characterization to a geomagnetic field model covering the historical era, we find that the mean SAA area increase and westward drift rates are twice slower than previously reported. Our results reveal that the SAA area and center are much more time-dependent, including episodes of area decrease, eastward drift and rapid southward drift. We interpret these special events in terms of the secular variation of relevant large-scale geomagnetic flux patches on the core-mantle boundary. Our characterization may be used as a constraint on Earth-like numerical dynamo models.