The displacement histories of the San Jacinto and southernmost San Andreas fault zones are constrained by offset data with ages in the range of 5 Ma to 5 ka. Apparent discrepancies between long- and short-term average displacement rates can be reconciled with a time-variable rate model. In this model, the displacement rate on the San Andreas decelerated from ∼35 mm/yr at 1.5 Ma to as low as 9 ± 4 mm/yr by 90 ka. Over this same time period, the rate on the San Jacinto fault zone accelerated from an initial value of zero to a rate of 26 ± 4 mm/yr. The data also imply that the rate of the San Andreas fault accelerated since ca. 90 ka, from ∼9 mm/yr to the modern rate of 27 ± 4 mm/yr, whereas the San Jacinto decelerated from 26 ± 4 mm/yr to the modern rate of 8 ± 4 mm/yr. The time scale of these changes is significantly longer than the earthquake cycle, but shorter than time scales characteristic of lithospheric-scale dynamics. The emergence of the San Jacinto fault zone ca. 1.5 Ma coincided with the development of a major restraining bend in the San Andreas fault zone, suggesting that the formation of new subparallel faults could be driven by conditions that inhibit displacement on preexisting faults.