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The streams that flow from Headwaters to Humboldt Bay are still home to native runs of threatened coho salmon, steelhead, and many amphibians such as the Pacific giant salamander, tailed frog, and Olympic salamander. The mammals that live in Headwaters include the California black bear, Pacific fisher, mountain lion, coyote, black-tail deer, flying squirrel and red tree vole. Birds include the northern spotted owl, marbled murrelet, osprey, goshawk, and migratory and resident songbird populations. Tree species in the forest include coast redwood, Douglas fir, grand fir, western red cedar, Pacific yew, western hemlock, madrone, red alder, tan oak, California bay laurel and vine maple. An abundance of plants and ferns blanket the forest floor.
These old-growth forests contain mycorrhizal fungi, invertebrates and microorganisms that cannot exist in cutover forestlands. Many of the species found in Headwaters are federally and/or state listed as endangered or threatened, and others are candidates for listing.

