I have no idea exactly why the Fish Lake lakers would be generally darker in color, however that darker coloring is more common with lake trout in the north, such as in Canada. They do have alot of variability in color.
"Back and sides usually dark green liberally sprinkled with whitish to yellowish (never pink or red) spots;
overall color varies from light green to gray, brown, dark green or nearly black; belly white; pale spots present on dorsal, adipose and caudal fins and usually on base of anal; sometimes orange-red on paired fins,
especially in northern populations; anterior edge of paired and anal fins sometimes with a white border. At spawning time, males develop a dark lateral stripe and become paler on the back (Ref. 27547). "
I'm going out on a limb here, but it could be that the fish in Fish Lake and in Flaming Gorge are from different ancestral populations of lake trout. Fish Lake was first stocked with Lake Trout over 100 years ago, in 1900 [url "http://wildlife.utah.gov/fishing/fish_lake/fish_lake_lake_trout.pdf"]http://wildlife.utah.gov/..._lake_lake_trout.pdf[/url] , and has been largely self sustaining ever since. Plantings have occurred, but a recent study showed that 97% of the Fish Lake lake trout had no adipose fin clippings (so they had not been stocked). Flaming Gorge was not completed until 1962. Supposedly, the Lake Trout in Flaming Gorge drifted down from the Green River drainage and then took hold [url "http://www.utahfishinginfo.com/utahlakes/flaminggorge.php"]http://www.utahfishinginfo.com/...kes/flaminggorge.php[/url].
The Fish Lake population of piscivorous lake trout eat mainly small rainbow trout. They used to eat chubs, but the illegal perch planting outcompeted the chubs and forced lakers to eat more trout. In contrast, the Flaming Gorge population of trophy lake trout eat mainly Kokanee. They could make a difference, but maybe not.
I do know that simple differences in dissolved minerals in the water and PH levels can make a difference in fish coloring.
Here are some pics of other dark lake trout from Canada.
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