Board Thread:Lore Discussion/@comment-13199219-20130809220651/@comment-98.239.192.193-20130809224120

I think it has something to do with necromancy or some relation to Oblivion. I know that the souls used in black soul gems are sent to the Soul Cairn, but I'm vaguely aware of some lore indicating the reason for the difference. It's either in a book or someone mentioned it at the College of Winterhold.

As for gameplay, black soul gems can hold any soul (even white ones) but they are more rare than regular soul gems, and don't really start appearing until later in the game. It would be rather unbalanced to be able to soul trap everything you found early in the game, especially since you encounter a lot more people than creatures.