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Moyle, P. B., & Cech J. J. (1996).  Fishes: An Introduction to Ichthyology. 590.
Moyle, P. B., & Cech J. J. (1982).  Fishes: An Introduction to Ichthyology. 593.
O'Rear, T., & Moyle P. B. (2014).  Fishes and aquatic macroinvertebrates. Suisun Marsh - ecological history and possible futures.
Moyle, P. B., & Yoshiyama R. M. (1992).  Fishes, aquatic diversity management areas, and endangered species: a plan to protect California's native aquatic biota. California Policy Seminar.
Moyle, P. B., Kennedy T., Kuda D., Martin L., & Grant G. (1991).  FISHES OF BLY TUNNEL, LASSEN COUNTY, CALIFORNIA. The Great Basin Naturalist. 51(3), 267-270.
Taylor, T. L., Moyle P. B., & Price DG. (1982).  Fishes of the Clear Lake Basin. (Moyle, P. B., Ed.).Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. Publications in Zoology . 115, 171–224.
Taylor, T. L., Moyle P. B., & Price DG. (1982).  Fishes of the Clear Lake Basin. (Moyle, P. B., Ed.).Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. Publications in Zoology . 115, 171–224.
Williamson, B. O., O'Rear T., De Carion D., Durand J. R., & Moyle P. B. (2016).  Fishes of the Nurse-Denverton Complex: managed wetlands and tidal waterways in Suisun Marsh. IEP Newsletter.
Moyle, P. B., & Daniels R. A. (1982).  Fishes of the Pit River System, McCloud River System, and Surprise Valley Region. (Moyle, P. B., Ed.).Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. Publications in Zoology. 115, 1-82.
Moyle, P. B., & Daniels R. A. (1982).  Fishes of the Pit River System, McCloud River System, and Surprise Valley Region. (Moyle, P. B., Ed.).Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. Publications in Zoology. 115, 1-82.
Katz, J., Jeffres C., Conrad L., Sommer T., Martinex J.., Brumbaugh S., et al. (2017).  Floodplain farm fields provide novel rearing habitat for Chinook salmon. PLoS ONE. 12(6), 
Opperman, J.J.., Moyle P. B., Larsen E.W.., Florsheim J.L.., & Manfree A.. D. (2017).  Floodplains: Processes and Management for Ecosystem Services. 258.
Kiernan, J. D., & Moyle P. B. (2012).  Flows, droughts, and aliens: factors affecting the fish assemblage in a Sierra Nevada, California, stream. Ecological Applications. 22(4), pp. 1146-1161.
Moyle, P. B., Li H. W., & Barton B. A. (1986).  The Frankenstein effect: impact of introduced fishes on native fishes in North America. (Stroud, R.. H., Ed.).Fish culture in fisheries management. 415–426.
Howard, J. K., Fesenmyer K., Grantham T. E., Viers J. H., Ode P., Moyle P. B., et al. (2018).  A Freshwater Conservation Blueprint for California: Prioritizing Watersheds for Freshwater Biodiversity. Freshwater Science. 37(2), 
Moyle, P. B., & Smith J. J. (1998).  Freshwater fishes of the Central California Coast. (Chiariello, N.., & Dasmann R.. F., Ed.).Symposium on biodiversity of the Central California Coast. 17-22.
Moyle, P. B. (2008).  The Future of Fish in Response to Large-Scale Change in the San Francisco Estuary, California. American Fisheries Society Symposium. 64,
Moyle, P. B., Manfree A. D., & Fiedler P. L. (2013).  The Future of Suisun Marsh as Mitigation Habitat. San Francisco Estuary and Watershed Science. 11(3), 
Moyle, P. B., & Bennett W. A. (2008).  The future of the delta ecosystem and its fish. Technical Appendix D to Lund, J., et al., Comparing futures for the Sacramento-San Joaquin delta. 38.
H
Durand, J. R., & Moyle P. B. (2011).  Habitat complexity and the ecology of flooding islands (polders) in the Sacramento-san Joaquin Delta, USA.
Young, M., Berridge K., O'Rear T., Moyle P. B., & Durand J. R. (2017).  Habitat partitioning by native and non-native fishes and decapods in novel habitats of the upper San Francisco Estuary. Biological Invasions.
Moyle, P. B., Lund J. R., Bennett W. A., & Fleenor W. E. (2010).  Habitat Variability and Complexity in the Upper San Francisco Estuary. San Francisco Estuary and Watershed Science. 8(3), 
Alley, D. W., Dettman DH., Li HW., & Moyle P. B. (1977).  Habitats of native fishes in the Sacramento River basin. (Sands, A.., Ed.).Riparian Forests in California: Their Ecology and Conservation Institute of Ecology Publication. 87-94.
Quiñones, R. M., Johnson M. L., & Moyle P. B. (2014).  Hatchery practices may result in replacement of wild salmonids: adult trends in the Klamath basin, California. Environmental biology of fishes. 97, 233–246.
Baxa, D. V., Stover A., Clifford M., Kurobe T., Teh S. J., Moyle P. B., et al. (2013).  Henneguya sp. in yellowfin goby Acanthogobius flavimanus from the San Francisco Estuary. SpringerPlus. 2, 420.
Yoshiyama, R. M., Fisher F. W., & Moyle P. B. (1998).  Historical Abundance and Decline of Chinook Salmon in the Central Valley Region of California. North American Journal of Fisheries Management. 18(3), 487-521.
Yoshiyama, R. M., Gerstung E. R., Fisher F. W., & Moyle P. B. (2001).  Historical and present distribution of Chinook salmon in the Central Valley drainage of California. (Brown, R. L., Ed.).Contributions to the Biology of Central Valley Salmonids. 71-176.
Yoshiyama, R. M., Gerstung E. R., Fisher F. W., & Moyle P. B. (1996).  Historical and present distribution of Chinook salmon in the Central Valley drainage of California. Sierra Nevada Ecosystem Project: Final report to Congress , Vol. III, assessments, commissioned reports, and background information. 3, 309-362.
Campbell, E. A., & Moyle P. B. (1991).  Historical and recent population sizes of spring-run chinook salmon in California. (Hassler, T. J., Ed.).Proceedings, Northeast Pacific Chinook and Coho Salmon Workshop. 155-216.
Yoshiyama, R. M., & Moyle P. B. (2010).  Historical Review of Eel River Anadromous Salmonids, with Emphasis on Chinook Salmon, Coho Salmon and Steelhead. PDF icon Eel River Final Report, Feb. 2010 (1.34 MB)
Marchetti, M. P., Light T.., Feliciano J., Armstrong T., Hogan Z., Viers J. H., et al. (2001).  Homogenization of California's Fish Fauna Through Abiotic Change. (Lockwood, J. L., & McKinney M. L., Ed.).Biotic Homogenization. 259-278.
Moyle, P. B., & Mount JF. (2007).  Homogenous rivers, homogenous faunas. Proceedings of the National Academy of Sciences. 104(14), 5711-5712.
Moyle, P. B., & Massingill M. (1981).  Hybridization between hitch, Lavinia exilicauda, and Sacramento blackfish, Orthodon microlepidotus, in San Luis Reservoir, California. California Fish and Game. 67, 196-198.
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Durand, J. R., Chandos A.., De Carion D., Fleenor W. E., Hobbs J. A., Montgomery J., et al. (2012).  Identifying Habitat Characteristics of the North Delta Arc.
Brown, L. R., & Moyle P. B. (1981).  The Impact of Squawfish on Salmonid Populations: A Review. North American Journal of Fisheries Management. 1(2), 104-111.
Parker, I.M.., Simberloff D.., Lonsdale W.M.., Goodell K.., Wonham M.., Kareiva P.M.., et al. (1999).  Impact: Toward a Framework for Understanding the Ecological Effects of Invaders. Biological Invasions. 1(1), 3-19.
Katz, J. V. E., Moyle P. B., Quiñones R. M., Israel J. A., & Purdy S. (2012).  Impending extinction of salmon, steelhead, and trout (Salmonidae) in California. Environmental Biology of Fishes.
Katz, J. V. E., Moyle P. B., Quiñones R. M., Israel J. A., & Purdy S. (2013).  Impending extinction of salmon, steelhead, and trout (Salmonidae) in California. Environmental Biology of Fishes. 96, 1169-1186.PDF icon Katz_et_al._2013 salmonids in CA.pdf (517.46 KB)
Hogan, Z. S., Moyle P. B., May B., M. Zanden J. Vander, & Baird I. G. (2004).  The Imperiled Giants of the Mekong: Ecologists struggle to understand—and protect—Southeat Asia's large migratory catfish. American Scientist. 92(3), 228-237.
Brown, L. R., Moyle P. B., Bennett W. A., & Quelvog B. D. (1992).  Implications of morphological variation among populations of California roach Lavinia symmetricus (Cyprinidae) for conservation policy. Biological Conservation. 62(1), 1 - 10.
Moyle, P. B. (1997).  The importance of an historical perspective: Fish introductions.. Fisheries. 22(10), 14.
Moyle, P. B., Kiernan J. D., & Williams J. G. (2011).  Improving Environmental Flow Methods Used in California Ferc Licensing.
Moyle, P. B. (1977).  In defense of sculpins. Fisheries . 2(1), 20-23.
Baltz, D. M., & Moyle P. B. (1982).  The influence of riparian vegetation on stream fish communities of California. (Warner, P.., & Hendrix H.., Ed.).California Riparian Systems. 183-187.
Baltz, D. M., Vondracek B., Brown L. R., & Moyle P. B. (1987).  Influence of Temperature on Microhabitat Choice by Fishes in a California Stream. Transactions of the American Fisheries Society. 116(1), 12-20.
Moyle, P. B. (1976).  Inland Fishes of California. 405.
Moyle, P. B. (2002).  Inland Fishes of California. Revised and expanded. 502.