The known active fault segments shown on the index map came from Figure 25 of USGS Open-File Report 96-532: "National Seismic Hazard Maps, June 1996: Documentation" by Arthur Frankel, Charles Mueller, Theodore Barnhard, David Perkins, E.V. Leyendecker, Nancy Dickman, Stanley Hanson, and Margaret Hopper.
For northern California, the potential sources of earthquakes larger than magnitude 6 are documented in Open-File Report 96-705 by the Working Group on Northern California Earthquake Potential (chaired by Jim Lienkaemper).
For the state as a whole, see "Probabilistic seismic hazard assessment for the State of California" by Petersen, M. D., Bryant, W.A., Cramer, C.H., Cao, T., Reichle, M.S., Frankel, A.D., Lienkaemper, J.J., McCrory, P.A., and Schwartz, D.P, 1996 (California Division of Mines and Geology Open-File Report 96-08; [published jointly as] U.S. Geological Survey Open-File Report 96-706).
The faults and fault zones described in these reports are known to have been active in the last 2 million years and are thought to pose a measurable hazard.
For California the faults on the individual zoomed-in and special maps come from the three categories of faults believed to have been active in the last 700,000 years shown on the "Preliminary Fault Activity Map of California" by C.W. Jennings (1992, California Division of Mines and Geology Open-File Report 92-03). This map has been superseded by Jennings, C.W., 1994, Fault activity map of California and adjacent areas, with locations and ages of recent volcanic eruptions: California Division of Mines and Geology, Geologic Data Map No. 6, map scale 1:750,000.
For Nevada the faults on the individual zoomed-in and special maps come from USGS Open-File Report 96-532 mentioned above.