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Both location and visually. Some of them are pretty easy to distinguish (Snakes and Colorados), while the two that look similar (Bonnies and Yellowstones) live in pretty distinct drainages.

Throw in this:

http://farm5.static.flickr.com/4103/5024125349_049346e0b8_b.jpg

This:

http://farm5.static.flickr.com/4154/5024777570_05bb715645_b.jpg

And this:

Yellowstone Cutthroat:

http://farm4.static.flickr.com/3199/2741097869_509bb6a185_b.jpg

Snake River Cutthroat:

http://farm5.static.flickr.com/4099/4771684325_6a41a98d12_b.jpg

Colorado...