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Little bitterroot up in the flathead. It takes a long time to ice up and the big fish are in 100 ft plus of water so it can be tough to find/hook them(or so I've been told, never fished it myself). I've seen pics though, there are some toads in there.
I typically fish for kokanee over deep water between 70 to 120 feet. Kokanee are almost always stratified in the water column feeding on various types of zooplankton, which are generally found higher in the water column and are suspended over deep water. You may find kokanee anywhere from 10-80 feet down so a flasher is a critical asset not only for locating fish, but it also ensures that your lure is being presented at the correct depth where the fish are located.
A typical kokanee rig is a big silver spoon, such as one from cheap lure, followed by a foot or a foot and a half of leader tipped with a small rocker-type lure with one or two maggots on it. Try a red rocker lure to start with, as that color seems to be most consistently successful, but experiment with other colors and with glow lures. Jerk on your line to make the spoon flip, flutter, and flash, which attracts kokanee. Kokanee bite very lightly. You will have most success if you are on a lake where you can see your lure and the kokanee down your hole when you are fishing in a dark ice shelter. This typically means that the kokanee are in the top 4-8 feet of the water. You can find those conditions at Georgetown Lake, fishing in water perhaps 20 feet deep, although so far this year in Georgetown Lake the kokanee have been down out of sight. On a good day when the kokanee are high enough to see, there will often be several kokanee milling around your lure, and darting in to nip at the lure. As the kokanee nip, you have to try to set the hook. Timing is critical. Even when you get your timing pretty good, you may only be hooking kokanee on a third of your attempts. But when sight fishing, you can catch a lot of fish. 50-80 fish days at Georgetown Lake, where there is no limit on kokanee, are not at all unusual. And you may pick up some trout as well. Kokanee have soft mouths, so don't try to set the hook too hard. Just quickly pull the kokanee to the surface and lift them out of the water.I'm lousy at fishing for kokanee when they are down out of sight, so I'll let somebody else explain techniques that work for that. If the fish are out of sight, a fishfinder which is sensitive enough to pick up a small rocker lure is very helpful, because it allows you to position your lure and flasher at the same depth as the kokanee schools. You can catch kokanee using a Jawjacker. Set up the jawjacker in a hole near the hole where you are actively jigging, so your jigging will attract kokanee both to your active lure and the lure on your jawjacker. The kokanee you want to catch are the ones which are going to spawn next fall, which are the biggest silver kokanee. When talking about kokanee, "big" is a relative thing - on most lakes in Montana, if you catch a 12 inch kokanee while ice fishing, you should report it to Boone and Crockett. Kokanee which are going to spawn in two years will be pretty small. In the early winter you may catch some Kokanee which spawned last fall, but haven't died yet. These "spawners" will be a mottled brownish maroon color, will have a long hooked jaw and a humped back, and will be bigger than the silver kokanee. They aren't very tasty either cooked or smoked, and most people throw them back.