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1996
Moyle, P. B., Yoshiyama R. M., & Knapp R. A. (1996).  Status of fish and fisheries. Sierra Nevada ecosystem project: Final report to Congress Vol. II, assessments, commissioned reports, and background information. 2, 953-973.
Castleberry, D., Cech J. J., Erman D., Hankin D., Healey M., Kondolf M., et al. (1996).  Uncertainty and instream flow standards. Fisheries. 21(8), 20–21.
Bennett, W. A., & Moyle P. B. (1996).  Where have all the fishes gone: interactive factors producing fish declines in the Sacramento-San Joaquin estuary. (Hollibaugh, J. T., Ed.).San Francisco Bay: the Ecosystem. 519-542.
1997
Leidy, R. A., & Moyle P. B. (1997).  Conservation Status of the World's Fish Fauna: An Overview. (Fiedler, P. L., & Kareiva P. M., Ed.).Conservation Biology For the Coming Decade. 187-227.
Moyle, P. B. (1997).  The importance of an historical perspective: Fish introductions.. Fisheries. 22(10), 14.
Brown, L. R., & Moyle P. B. (1997).  Invading species in the Eel River, California: successes, failures, and relationships with resident species. Environmental Biology of Fishes. 49(3), 271-291.
Moyle, P. B., & Yoshiyama R. M. (1997).  The role of adaptive management in restoring chinook salmon to the Tuolumne River. (Wang, S. S. Y., & Carstens T., Ed.).Environmental and Coastal Hydraulics: Protecting the Aquatic Habitat. 557-562.
1998
Trenham, P. C., H. Shaffer B., & Moyle P. B. (1998).  Biochemical Identification and Assessment of Population Subdivision in Morphologically Similar Native and Invading Smelt Species (Hypomesus) in the Sacramento-San Joaquin Estuary, California. Transactions of the American Fisheries Society. 127(3), 417-424.
Viers, S. D., Opler P. A., Gilmer D. S., Graber D. M., Graham T., Huckaby L. S., et al. (1998).  California. (Mac, M. J., Opler P. A., Haecker C. E. Puckett, & Doran P. D., Ed.).Status and trends of the nation’s biological resources. 1 & 2, 593-603.
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., & Randall P. J. (1998).  Evaluating the Biotic Integrity of Watersheds in the Sierra Nevada, California. Conservation Biology. 12(6), 1318–1326.
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.
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., & 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.
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.
Moyle, P. B. (1998).  Review of “Fisheries Conservation and Management” by M. R. Ross. Copeia .
Moyle, P. B. (1998).  Review of “Web of Water: Life in Redwood Creek” by M. Khosla. California Coast and Ocean . 14(1), 
Healey, M., Kimmerer W., Kondolf GM., Meade R., Moyle P. B., & Twiss R. (1998).  Strategic plan for the Ecosystem Restoration Program. 252.
1999
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. (1999).  Effects of invading species on freshwater and estuarine ecosystems. Invasive species and biodiversity management. 177-191.
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.
Li, H. W., & Moyle P. B. (1999).  Management of introduced fishes. (Kohler, C. C., & Hubert W. A., Ed.).Inland fisheries management in North America. 345-274.
2000
Moyle, P. B. (2000).  Aliens in fresh water. Review of R. Claudi and J. H. Leach, eds. 2000. Non-indigenous freshwater organisms: vectors, biology, and impacts. . Ecology . 81, 2945-2946.
Yoshiyama, R. M., Moyle P. B., Gerstung E. R., & Fisher F. W. (2000).  Chinook Salmon in the California Central Valley: An Assessment. Fisheries. 25(2), 6-20.
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. (2000).  Restoring aquatic ecosystems is a matter of values. California Agriculture. 54(2), 16–25.
Marchetti, M. P., & Moyle P. B. (2000).  Spatial and Temporal Ecology of Native and Introduced Fish Larvae in Lower Putah Creek, California. Environmental Biology of Fishes. 58(1), 75-87.
2001
Sommer, T., Harrell B., Nobriga M., Brown R. L., Moyle P. B., Kimmerer W., et al. (2001).  California's Yolo Bypass: Evidence that flood control Can Be compatible with fisheries, wetlands, wildlife, and agriculture. Fisheries. 26(8), 6-16.
Baird, I., Hogan Z., Phylaivanh B., & Moyle P. B. (2001).  A Communal Fishery for the Migratory Catfish Pangasius macronemain the Mekong River. Asian Fisheries Science. 14, 25–41.
Marchetti, M. P., & Moyle P. B. (2001).  Effects of Flow Regime on Fish Assemblages in a Regulated California Stream. Ecological Applications. 11(2), 530-539.
Chasnoff, B., & Moyle P. B. (2001).  Ethics, ecology, and economics in river management: the benefits of working together. (K, D. C., & McGinn R. E., Ed.).Navigating rough waters: ethical issues in the water industry. 157-176.
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.
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., & Davis L. H. (2001).  A list of freshwater, anadromous, and euryhaline fishes of California. California Fish and Game. 86(4), 244–258.
Sweetnam, D.S., Baxter R.D., & Moyle P. B. (2001).  True smelts. (Leet, W. S., Dewees C. M., Klingbeil R., & Larson E. J., Ed.).California's Living Marine Resources: A Status Report. 472–479.
2002
Moyle, P. B. (2002).  Inland Fishes of California. Revised and expanded. 502.
Matern, S. A., Moyle P. B., & Pierce L. C. (2002).  Native and Alien Fishes in a California Estuarine Marsh: Twenty-One Years of Changing Assemblages. Transactions of the American Fisheries Society. 131(5), 797-816.
2003
Moyle, P. B., Crain P. K., Whitener K., & Mount JF. (2003).  Alien Fishes in Natural Streams: Fish Distribution, Assemblage Structure, and Conservation in the Cosumnes River, California, U.S.A.. Environmental Biology of Fishes. 68(2), 143-162.
Feyrer, F., Herbold B., Matern S. A., & Moyle P. B. (2003).  Dietary shifts in a stressed fish assemblage: Consequences of a bivalve invasion in the San Francisco Estuary. Environmental Biology of Fishes. 67(3), 277-288.
Moyle, P. B. (2003).  Eagle Lake rainbow trout: survivors in a troubled habitat. Streamkeepers Log . 104,
Moyle, P. B. (2003).  Goose Lake redband trout: high desert survivors. Streamkeepers Log . 103,
Moyle, P. B. (2003).  Review of Candiru: life and legend of bloodsucking catfishes by Stephen Spotte. Fisheries . 28(1), 
2004
Marchetti, M. P., Moyle P. B., & Levine R. (2004).  Alien Fishes in California Watersheds: Characteristics of Successful and Failed Invaders. Ecological Applications. 14(2), 587-596.
Moyle, P. B., Baxter R. D., Sommer T., Foin T. C., & Matern S. A. (2004).  Biology and Population Dynamics of Sacramento Splittail (Pogonichthys macrolepidotus) in the San Francisco Estuary: A Review. San Francisco Estuary and Watershed Science. 2(2), 1-47.
Lewis, W. A., Adams R. M., Cowling E.B., Helfman E. S., .D.D.Howard C., J H. R., et al. (2004).  Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. 334.
Marchetti, M. P., Light T., Moyle P. B., & Viers J. H. (2004).  Fish Invasions in California Watersheds: Testing Hypotheses Using Landscape Patterns. Ecological Applications. 14(5), 1507-1525.
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.
Marchetti, M. P., Moyle P. B., & Levine R. (2004).  Invasive species profiling? Exploring the characteristics of non-native fishes across invasion stages in California. Freshwater Biology. 49(5), 646–661.
Moyle, P. B. (2004).  Review of Snakehead: fish out of water by Jay Dolan. CoCopeia . 710-711.
Cohen, A. N., & Moyle P. B. (2004).  Summary of data and analyses indicating that exotic species have impaired the beneficial uses of certain California waters.