Overwatch – Unlocking Origin Skins from Loot Boxes

So far, every piece of unlockable loot comes from the loot boxes (and/or bought from coins) with the exception of the Pre-order and Origins edition skins. (I'm betting there will be a Blizzcon 2016 one as well)

According to wiki,

Each Loot Box contains four random items that can be used to customize the appearance of heroes. Items come in common, rare, epic, and legendary quality levels, and every Loot Box includes at least one rare quality or better item.

and,

even unopened Loot Boxes will glow in a color corresponding to what items are inside.

so if you haven't gotten a box before with a different glow, you just were unlucky that you hadn't gotten as rare of items in your previous loot boxes.