Storing and getting bounding boxes.

Right now, the way I store bounding boxes in my game is in a 1 dimensional array, then when I want to check if there is a bounding box at a certain position, I loop through all of the bounding boxes, and if one matches, return it. That just seems really inefficient to me, and I was wondering if there was a better way to store and find bounding boxes (finding preferably within the bounding box area).

Don’t fix it if it isn’t broken.

That said, something like a HashMap<Point, BoundingBox> might work, your problem description is pretty vague.
There are also more advanced things like R-trees.

aye, a map of points would be something like a cell partition.

another way to handle boxes could be a box-tree : http://en.wikipedia.org/wiki/R-tree

Keeping them sorted on 1 axis is a very simple solution that, for a sparsely populated domain, can be very efficient.