If you really can't find them, quit the game and then return to it, but when game will ask you if you want to continue saved game - click "No". This way you will restart Witch Istalnd and when you will play it again roots will be in deifferent places so chances are they will be located in places easier to find.
Also please note that roots marked by violet and green circles are almost invisible so you just need to click in that areas.
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Yaroslav Yanovsky - Producer / Game Designer at Enkord
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