+4  A: 
StyleManager.getStyleDeclaration("Application").setStyle('backgroundColor', 'Red');
Nathan Mische
This is how the [Flex 3 Style Explorer](http://examples.adobe.com/flex3/consulting/styleexplorer/Flex3StyleExplorer.html) works, but I'm not yet able to get it working in my application. Going to dig in further to see if there's something else preventing it from working.
Adam Tuttle
I ended up removing the `backgroundColor`/`backgroundGradientColors` definitions from my application tag, and setting the color explicitly to be one or the other in onApplicationComplete. Doing that, this solution worked perfectly.
Adam Tuttle
+1  A: 

It looks like if your mx:Application tag uses the backgroundColor attribute you need to do this:

mx.core.Application.application.setStyle('backgroundColor','green');
Nathan Mische