You get them by doing good DoN missions, Ebon crystals by doing evil ones. They are like LDoN points except they are tradable. You use them to purchase armor, augments and spells from the DoN merchant, which are no trade.
The DoN good/evil missions are given in Lavastorm, after you do tasks to get your faction up. You can also be in a group where someone with a higher faction gets the missions. Each mission you also get a no trade item that you can either destroy, or turn in for more faction, depending on whether you want good or evil, so you can take both kinds of missions.