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I'm using the Boadilla theme with Beaver colortheme. All the colored stuff are in dark red as they should be, except for the bibliography item: they still use the structure color that is the classical blue. I can get rid of this by manually changing the color, except from the bibliography number item, that is still in blue.

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You don't specify how you generate the bibliography. However if you use the standard bibliography environment from beamer, you can use beamer's color setting scheme. Simply add

\setbeamercolor{bibliography item}{parent=palette primary}
\setbeamercolor*{bibliography entry title}{parent=palette primary}

(The * is necessary in the second command.)

Similarly, you can set the colors bibliography entry author, bibliography entry journal and bibliography entry note. If you want to set the color explicitly instead of using the color from the theme, use {fg=⟨color⟩} instead of {parent=...}.

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