The north end of the Pioneer Mountains is underlain by the following rocks: lower Proterozoic gneiss and amphibolite; middle proterozoic clastic rocks of the Missoula Group (Mount Shields Formation?); basal Cambrian clastic unit; Cambrian-Devonian-Carboniferous shelf sequence; Permian Phosphoria Formation; and Lower Triassic Dinwoody Formation. Jurassic rocks are missing. The Lower Cretaceous Kootenai Formation is of lagoonal to fluviatile facies, overlain by a thick (^approx 2 km, 1 mi) section of fluviatile Colorado Group. An upper member of the Colorado Group has yielded a Campanian-to-Maestrichtian pollen flora. The sedimentary rocks are cut by calc-alkalic plutonic rocks (80 to 65 m.y.B.P.), the oldest of which are synchronous with upper Colorado sedimentation. The y ungest pre-Quaternary rocks are Eocene and Oligocene calc-alkalic lavas and Oligocene pumiceous tuff. The Missoula Group is entirely in thrust sheets that postdate the Colorado, so the thrusting is no older than Campanian, but the thrusts are cut by 72 to 74 m.y.B.P. plutons. The Johnson thrust of Fraser and Waldrop, on the 1972 U.S. Geological Survey Geologic Quadrangle Map 988, is part of this thrust system. A klippe of Missoula Group on Morrison Hill is an erosional remnant, but most of the overthrust rocks are west of the Wise River valley and probably overlie Phanerozoic strata.

In addition to the thrust sheets, two families of high-angle faults dominate. One family trends west-northwest and displacements along these faults can be measured in kilometers. The Johnson thrust is interpreted to have been displaced by a sinistral fault of this system along the straight valley of Big Hole River between Seymour Creek and Dewey. The eastward projection of the mountain front at Maiden Rock, just south of Divide, resulted from block displacement along two strands of this fault. This particular fault is of major significance because it marks an abrupt jump in the initial strontium ratios of intrusive rocks, from values typical of the Boulder batholith (0.706 to 0.709) to those of the Pioneer batholith (0.711 to 0.716), indicating that different crustal blocks were juxta osed. The second family of high-angle faults trends north-northeast. Wise River valley is interpreted to be a graben in this system. One important fault in the system is the Fourth of July fault, with downdrop (to west) of several kilometers; the fault may be continuous with the Comet Mountain fault. The west-northwest fault system began at least before the Eocene lava flows, but complex field relations between the two high-angle fault systems indicate their growth must have overlapped in age, possibly through the late Tertiary.

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