I've found out you can get Utopium by tapping on trees and by buying it with real money. Are there any other ways?
You can also get Utopium daily from the Utopium mine (the first building reward you get). You have to tap it to show the building details and press the button that says "It's mine".
If you have the Sheriff's office, you can find one Utopium hiding among the credits.
If you have the Police Station, you can collect Utopium for clearing achievements.
Most of your Utopium will probably come from collecting hearts - every time you fill up all the hearts, you can get an animal gene, some coins, or 1 or 2 units of Utopium.
I'm sure there must be more buildings that give bonuses, but this is all I've encountered so far.