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I'm not sure if it is possible, as the GUI may have more capabilities than the terminal (yes, I've seen GUI terminals with only 16 colors very recently). It may depend on how the terminal is set. At any rate I would play with Color Theme.
Anyway, why are you using Emacs in both, the terminal and the GUI? Generally people find one or the other appealing and use only that one. If you are using Emacs remotely, maybe you want to run it locally and use Tramp to open files remotely, or as root.