Like most paleontological reconstructions coloration is pure speculation. In some rare cases clues to coloration are found in the fossil record (there's been a lot of work involving the color pigments in fossilized feathers). Typically though, the artist exercises his or her creative license. It's not an entirely blind guess, as some plausible reasoning is used.
Here I have explored several different color schemes for Bothriolepis. They are partially fanciful and partially based on contemporary fish living in similar environments and with similar ecological roles. Bothriolepis spent some of its time in freshwater environments, so it might have had a cryptic coloration to blend in with the sediment. The trout-like coloration (5th from the left) is my current favorite due to the subtle use of color.
Here are some modern day fish (mostly armored catfish) that I've been drawing upon for inspiration.
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