The San Juan Islands of Washington State form a geologically complex province located between the north Cascades, Vancouver Island, and the Olympic Peninsula. We have obtained 53 fission-track dates from the San Juan Islands province that help constrain its late Paleozoic to early Cenozoic tectonic and sedimentary history and its relationship to neighboring geologic terranes. The San Juan Islands can be divided into two main blocks separated by the Haro fault. South of the Haro fault, complexly deformed, metamorphosed, and probably exotic early Paleozoic to early Late Cretaceous rocks form four imbricate thrust plates separated by south- and east-dipping late Early to Late Cretaceous thrust faults. Reset zircon fission-track dates indicate that thrusting may have produced an upside-down geothermal gradient in the uppermost plate, the Decatur terrane. If present, this gradient was probably produced by conductive or frictional heating associated with a now-eroded overlying thrust fault and hot thrust plate. Cretaceous thrusting in the southern San Juan Islands was accompanied by uplift and resetting of apatite fission-track dates. In contrast to correlative rocks of the southern San Juan Islands, Upper Triassic to Lower Cretaceous rocks in and north of the Haro fault zone are essentially unmetamorphosed and only broadly folded. Apatite dates from the Upper Triassic Haro Formation and the Upper Jurassic and Lower Cretaceous Spieden Group indicate they did not participate in Late Cretaceous uplift of the southern San Juan Islands. Together with their basement (the Wrangellia terrane?), these rocks probably acted as a backstop to thrusting. The synorogenic Late Cretaceous Nanaimo basin formed north of the Haro fault in front of the advancing San Juan Islands thrust system. The age of Nanaimo deposition matches uplift (apatite) dates in the southern San Juan Islands, and detrital zircons from the Nanaimo Group yield dates consistent with southern San Juan Islands sources. Burial led to resetting of apatite dates in what is probably the deeper part of the Nanaimo basin.