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Moyle, P. B., & Leidy R. A. (1992).  Loss of Biodiversity in Aquatic Ecosystems: Evidence from Fish Faunas. (Fiedler, P. L., & Jain S. K., Ed.).Conservation Biology: The Theory and Practice of Nature Conservation, Preservation, and Management. 128-169.
Moyle, P. B. (1974).  Status of the Modoc sucker (Catostomus microps, Pisces: Catostomidae). Cal-Neva Wildlife. 1974, 35–38.
Moyle, P. B., & Marchetti M. P. (2006).  Predicting Invasion Success: Freshwater Fishes in California as a Model. BioScience. 56(6), 515-524.
Moyle, P. B. (1981).  Review of E. K. Balon (Editor), Charrs, salmonid fishes of the Genus Salvelinus. Transactions of the American Fisheries Society . 110, 313-316.
Moyle, P. B. (1984).  America's carp. Natural History. 93(9), 42-51.
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.
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. (1969).  Comparative Behavior of Young Brook Trout of Domestic and Wild Origin. The Progressive Fish-Culturist. 31(1), 51-56.
Moyle, P. B., & Marchetti M. P. (1999).  Applications of indices of biotic integrity to California streams and watersheds. (Simon, T. P., & Hughes R., Ed.).Assessing the sustainability and biological integrity of water resources using fish communities. 367–380.
Moyle, P. B., & Randall P. J. (1996).  Biotic integrity of watersheds. Sierra Nevada Ecosystem Project: Final report to Congress Vol. II, assessments, commissioned reports, and background information. 2, 975-985.
Moyle, P. B., Hobbs J., & Durand J. R. (2018).  Delta Smelt and the Politics of Water in California. Fisheries. 43,
Moyle, P. B., & Cech J. J. (1982).  Fishes: An Introduction to Ichthyology. 593.
Moyle, P. B., Manfree A. D., & Fiedler P. L. (2014).  Suisun Marsh: Ecological History and Possible Futures. 256.
Moyle, P. B. (2008).  Serpentine haiku. California Coast and Ocean. 24(2), 40.
Moyle, P. B. (1998).  Channelization (p. 121) and Dams, effects of (p. 170). (Calow, P., Ed.).Encyclopedia of Ecology and Environmental Management. 121, 170.
Moyle, P. B., & Yoshiyama R. M. (1994).  Protection of Aquatic Biodiversity in California: A Five-tiered Approach. Fisheries. 19(2), 6-18.
Moyle, P. B. (1976).  Some effects of channelization on the fishes and invertebrates of Rush Creek, Modoc County, California. California Fish and Game. 62, 179–186.
Moyle, P. B., Bennett W. A., Durand J. R., Fleenor W. E., Gray B. E., Hanak E., et al. (2012).  Where the Wild Things Aren’t Making the Delta a Better Place for Native Species. Public Policy Institute of California.
Moyle, P. B. (1991).  Ecology of introduced fishes and aquatic invertebrates in North America. (Yount, J. D., Ed.). 1-3.
Moyle, P. B., & Moyle M. A. (1991).  Introduction to fish imagery in art. Environmental Biology of Fishes. 31(1), 5-23.
Moyle, P. B. (1973).  Recent changes in the fish fauna of the San Joaquin River system. Cal-Neva Wildlife. 1973, 60–63.
Moyle, P. B. (2002).  Inland Fishes of California. Revised and expanded. 502.
Moyle, P. B., & Baltz D. M. (1979).  Stillwaters west. Rod and Reel Magazine . Part I, September/October; Part II, November/December, Part I pp20-26; Part II pp22-27.
Moyle, P. B., & Vondracek B. (1985).  Persistence and Structure of the Fish Assemblage in a Small California Stream. Ecology. 66(1), 1-13.
Moyle, P. B., Katz J. V. E., & Quiñones R. M. (2011).  Rapid decline of California’s native inland fishes: A status assessment. Biological Conservation. 144(10), 
Moyle, P. B. (2012).  Review of An entirely synthetic fish: how rainbow trout beguiled America and overran the world by Anders Halverson. Quarterly Review of Biology . 87(168), 
Moyle, P. B., Pine R., Brown L. R., Hanson C.H., Herbold B., Lentz K.M., et al. (1996).  Recovery plan for the Sacramento-San Joaquin Delta native fishes. 193.
Moyle, P. B. (2003).  Review of Candiru: life and legend of bloodsucking catfishes by Stephen Spotte. Fisheries . 28(1), 
Moyle, P. B., & Cech J. J. (1996).  Fishes: An Introduction to Ichthyology. 590.
Moyle, P. B., Smith J. J., & Baltz D. M. (1982).  A Review. (Moyle, P. B., Ed.).Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. Publications in Zoology . 115, 255-256.
Moyle, P. B., Marchetti M. P., Baldrige J., & Taylor T. L. (1998).  Fish health and diversity: Justifying flows for a California stream. Fisheries. 23(7), 6-15.PDF icon PutahCRFisheries98.pdf (632.16 KB)
Moyle, P. B., & Li H.W. (1994).  Nuisance essay: good report but should go much farther. Fisheries. 19, 22-23.
Moyle, P. B., Herbold B., Stevens D. E., & Miller L. W. (1992).  Life History and Status of Delta Smelt in the Sacramento-San Joaquin Estuary, California. Transactions of the American Fisheries Society. 121(1), 67-77.
Moyle, P. B., & Marciochi A. (1975).  Biology of the Modoc Sucker, Catostomus microps, in Northeastern California. Copeia. 1975(3), 556-560.
Moyle, P. B., & Mount JF. (2007).  Homogenous rivers, homogenous faunas. Proceedings of the National Academy of Sciences. 104(14), 5711-5712.
Moyle, P. B., & F Senanayake R. (1982).  Wildlife conservation in Sri Lanka: a Buddhist dilemma.. Tigerpaper. 9(4), 1-4.
Moyle, P. B. (1984).  Review of W. N. Eschmeyer and E. S. Herald, A Field Guide to Pacific Coast Fishes of North America from the Gulf of Alaska to Baja California. The Quarterly Review of Biology. 59, p. 85.
Moyle, P. B., & Herbold B. (1987).  Life-history patterns and community structure in stream fishes of western North America: Comparisons with eastern North America and Europe. (Matthew, W. J., & Heins D. C., Ed.).Community and Evolutionary Ecology of North American Stream Fishes. 25-32.
Moyle, P. B., Crain P. K., & Whitener K. (2007).  Patterns In The Use Of A Restored California Floodplain By Native And Alien Fishes. San Francisco Estuary and Watershed Science. 5(3), 
Moyle, P. B., & Bacon J. (1969).  Distribution and abundance of molluscs in a freshwater environment. Journal of the Minnesota Academy of Science. 35, 82–85.
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. (1996).  Potential aquatic diversity management areas. Sierra Nevada Ecosystem Project: Final report to Congress Vol. II, assessments, commissioned reports, and background information. 2, 1493-1503.
Moyle, P. B., Lusardi R. A., Samuel P., & Katz J. V. E. (2017).  State of the Salmonids: Status of California's Emblematic Fishes 2017. PDF icon State of the Salmonids 2017 (8.35 MB)
Moyle, P. B., Vondracek B., & Grossman G. D. (1983).  Responses of Fish Populations in the North Fork of the Feather River, California, to Treatments with Fish Toxicants. North American Journal of Fisheries Management. 3(1), 48-60.
Moyle, P. B., Quiñones R. M., & Brown L. R. (2010).  Status and conservation of lampreys in California.
Moyle, P. B. (2008).  Protecting migration routes. Issues in Science and Technology. 24 (summer)(4), 
Moyle, P. B. (2000).  Connecting the land to the sea: anadromous fishes. (Abell, R. A., & 10 others., Ed.).Freshwater Ecoregions of North America: a Conservation Assessment. 46-47.
Moyle, P. B. (1994).  Biodiversity, biomonitoring, and the structure of stream fish communities. (Loeb, S., & Spacie A., Ed.).Biological monitoring of aquatic systems. 171–186.
Moyle, P. B. (1977).  In defense of sculpins. Fisheries . 2(1), 20-23.
Moyle, P. B., Hobbs J., & O'Rear T. (2012).  Fishes. Ecology, Conservation, and Restoration of Tidal Marshes: The San Francisco Estuary. 161-173.