Whiskeytown is home to a wide variety of mushroom species, but a complete inventory has not yet been conducted. With the help of Dr. Susan Libonati-Barnes and her students from Shasta College, park staff and visitors are learning much more about these essential members of the park's forest communities.
Native tree diseases and decay fungi are common in Whiskeytown. In 2005, Dr. Robert Mathiasen of Northern Arizona University conducted an extensive inventory of root, rust, and foliage diseases; blights; stem decays; mistletoes; and bacterial tree diseases as part of the Sabbatical in the Parks program. This inventory documented 21 native and 2 non-native disease species in the park.