The seismically active Pajarito fault system (PFS) of northern New Mexico, United States, is a complex zone of deformation made up of many laterally discontinuous faults and associated folds and fractures that interact in ways that have important implications for seismic hazards. Mapping and drilling projects in the PFS provide new insights into the structural geometry and paleoseismic history of the fault system. A 1.25 Ma old datum (the Bandelier Tuff) and high-resolution digital elevation data allow construction of throw-length profiles along the entire length of the PFS, revealing primary geometric features previously unrecognized. The fault system as a whole consists of numerous closely spaced overlapping sections ~8–14 km long. Slip maxima in some cases occur near the centers of these sections, and in others they are shifted toward one end. Along-strike asymmetrical throw profiles and throw deficits indicate fault branching, merging, and strain transfer. This pattern results from processes of fault linkage and conservation of strain on diverse structures of a large fault system. New mapping reveals that the northern end of the Pajarito fault terminates in a wide zone of extensional monoclines and discontinuous, small-displacement faults, and interacts with nearby antithetic faults. New paleoseismic data from a normal fault splay, interpreted in light of previous paleoseismic work, argue for three Holocene surface-rupturing earthquakes; one ca. 1.4 thousand calendar years ago (1.4 cal ka) on the Pajarito fault, a second 6.5–5.2 ka ago on the Pajarito fault that is consistent with an event 6.5–4.2 ka ago on the Guaje Mountain fault, and a third ca. 9 ka ago on both the Pajarito and the Rendija Canyon faults. This paleoseismic event chronology demonstrates that the Pajarito fault often ruptures alone, but sometimes ruptures either with the Rendija Canyon or the Guaje Mountain fault. When this occurs, the resultant seismic moment and therefore the earthquake magnitude are larger than when the main Pajarito fault ruptures alone. Evidence for fault interaction, and the presence of prominent bends in the Pajarito fault system, imply structural control of paleoseismicity and neoseismicity and suggest the potential for stress concentrations and earthquake triggering in complex linking fault systems.