We determine the crustal and upper mantle structure of southern South America by inverting regional seismograms recorded by the Seismic Experiment in Patagonia and Antarctica. We present a waveform inversion method that utilizes a niching genetic algorithm. The niching genetic algorithm differs from the traditional genetic algorithm in that the inversion is performed in multiple subpopulations, thus generating a broader search of the model space and enabling us to examine alternative local error minima. The vertical and transverse waveforms were used, extending from the P arrival to the surface waves, and the inversion was performed at either 0.005--0.06 Hz (larger events) or 0.02--0.06 Hz (smaller events). The inversion included anisotropy by solving for separate SV and SH structures in the upper mantle. Results indicate that crustal thickness varies from 26 to 36 km with thicker values toward the northeast, suggesting that there is little crustal thickening beneath the austral Andes. The average upper mantle velocities are similar to the preliminary reference Earth model (PREM) except that the southernmost region shows velocities of 5% slower than PREM. The upper mantle has up to 5% polarization anisotropy between the Moho and 120 km depth. The strongest anisotropy is localized in a lithospheric lid shallower than 65 km depth, which overlies a pronounced low-velocity zone. This shallow limit to anisotropy is consistent with the relatively small shear wave splitting values found in this region. These results suggest that the anisotropy is limited to lithospheric depths and may imply the absence of a strong mantle flow pattern in the asthenosphere.