There are 2 options in PyCharm to set the environment colors:
Appearance & Behaviour > Appearance > UI Options > Theme
Editor > Colors & Fonts > Scheme
I changed the latter to a dark theme, and got a dialog asking me if I wanted to change it for the UI as well - with an additional box to not ask me again. I checked the box and clicked yes. Subsequently, every time I change one of the options, the other one changes as well.
I changed my mind and want to have them separate: How can I decouple these options again?
Using PyCharm 2017.1
You can change this setting by editing the value in the file %USER%\\.PyCharmCE2017.1\config\options\options.xml
<property name="change.laf.on.editor.theme.change" value="false" />