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Understanding the long-term patterns of great earthquake rupture along a subduction zone provides a framework for assessing modern seismic hazard. However, evidence that can be used to infer the size and location of past earthquakes is typically erased by erosion after a few thousand years. Meter-scale cracks that cut the surface of coastal areas in northern Chile and southern Peru preserve a record of earthquakes spanning several hundred thousand years owing to the hyperarid climate of the region. These cracks have been observed to form during and/or shortly after strong subduction earthquakes, are preserved for long time periods throughout the Atacama Desert, demonstrate evidence for multiple episodes of reactivation, and show changes in orientation over spatial scales similar to the size of earthquake segments. Our observations and models show that crack orientations are consistent with dynamic and static stress fields generated by recent earthquakes. While localized structural and topographic processes influence some cracks, the strong preferred orientation over large regions indicates that cracks are primarily formed by plate boundary-scale stresses, namely repeated earthquakes. We invert the crack-based strain data for slip along the well-known Iquique seismic gap segment of the margin and find consistency with gravity anomaly-based inferences of long-term earthquake slip patterns, as well as the magnitude and location of the November 2007 Tocopilla earthquake. We suggest that the meter-scale cracks can be used to map characteristic earthquake rupture segments that persist over many seismic cycles, which encourages future study of cracks and other small-scale structures to better constrain the persistence of asperities in other arid, tectonically active regions.