Abstract Geological and geophysical research in upstate New York, with few exceptions, has not definitively associated seismicity with specific Proterozoic basement or Paleozoic bedrock structures. The central part of the Clarendon–Linden fault system (CLFS) between Batavia and Dale, NY is one of those exceptions where seismicity has been studied and has been spatially associated with structure. The CLFS is either a complex system of long faults with associated shorter branches and parallel segments, or a region of many short faults aligned north–south from the Lake Ontario shore southward to Allegany County, NY. Interpretation of 38 km of Vibroseis and approximately 56 km of conventional seismic-reflection data along 13 lines suggests that the CLFS is a broad zone of small faults with small displacements in the lower Paleozoic bedrock section that is at least 77 km long and 7–17 km wide and spatially coincident with a north-trending geophysical (combined aeromagnetic and gravity) lineament within the basement. The relative offset across the faults of the system is more than 91 m near Attica, NY. The CLFS is the expression of tectonic crustal adjustments within the Paleozoic rock above the boundary of two basement megablocks of differing petrologic provinces and differing earthquake characteristics that forms the eastern side of the Elzevir–Frontenac boundary zone. Deep seismic-reflection profiles display concave-eastward listric faults that probably merge at depth near the mid-crustal boundary layer. An interpretive vertical section provides the setting for refined definitions of the CLFS, its extensions at depth and its relation to seismicity. Most modern seismicity in western New York and the Niagara Peninsula of Ontario occurs in apparent patterns of randomly dispersed activity. The sole exception is a line of seven epicenters of small earthquakes that trend east from Attica, NY into the Rochester basement megablock. Earthquakes may be triggered at the intersections of north- and east-trending brittle faults within the Niagara basement megablock. Current interpretations of the mechanisms for earthquake generation in western New York and the Niagara Peninsula of Ontario require conservative estimates of seismic hazards that assume that an earthquake the size of the 1929 Attica, NY, event ( M b=5.2) or larger could occur anywhere in the Eastern Great Lakes Basin (EGLB). The broad zone of small-displacement faults that marks the CLFS in the lower Paleozoic sedimentary section and the uppermost basement may not provide the structural environment for generation of earthquakes in western New York. If this interpretation is correct, most seismicity is generated within the Niagara basement megablock beneath or west of the CLFS. Consequently, we may have to look to the deeper tectonic regime of basement megablocks to understand the distribution of modern seismicity in the EGLB.