We examine the structural complexities of a 28-km long part of the Clark fault of the San Jacinto fault zone in southern California in order to better document its lateral extent and the style of deformation of its southeast end. Changes in structural style are observed as the Clark fault’s damage zone widens from ~ 1-2 km in crystalline rocks of the Peninsular Ranges southeastward to ~ 18 km in the sedimentary rocks of the San Felipe-Borrego subbasin of the Salton Trough. The Clark fault extends into the San Felipe-Borrego subbasin as the Arroyo Salada segment for ~ 11-12 km to a newly defined northeast-trending structural boundary. This structural boundary, referred to herein as the Pumpkin Crossing block, is a ~ 3-km wide and ~ 8-km long fault zone dominated by northeast-striking sinistral-normal strike-slip faults. Southeast of the Pumpkin Crossing block the newly defined San Felipe Hills segment extends the Clark fault another ~12-13 km southeast to its intersection with the Extra fault zone. The Clark fault may have nearly 14.5-18 km of right separation represented in the surface deformation of the Arroyo Salada and San Felipe Hills segments, but the total amount of strain is masked by the wide diffuse fault zone with its complex deformation patterns and geometries. The lateral change observed in microseismicity patterns across the Arroyo Salada and San Felipe Hills segment boundary supports our structural interpretations about the existence, location, and structure of this boundary. Vertical patterns in the microseismicity suggest that the Clark fault zone narrows at depth, dips steeply northeast in the subsurface, and must interact with at least one weak decollement layer(s) beneath and/or with the sedimentary basin. Structural deformation within the late Miocene to Holocene silty- and clay-rich sedimentary basin of the Salton Trough includes features characteristic of strike-slip faults, such as stepovers, conjugate faults, folds, flower structures, and fault bends, as well as many unique structures that include pooch structures, ramp-flat geometries of strike-slip faults, complex en echelon fault zones with localized shear distributed across a high frequency network of faults, and heterogeneous kinematic indicators within individual fault zones.