The San Juan Islands of northwest Washington State comprise a diverse assemblage of Paleozoic and Mesozoic terranes amalgamated during a regional Cretaceous orogenic event. Detailed tectono-stratigraphy of the sedimentary cover to the Fidalgo Complex indicates the presence of several stratigraphically distinct units, which are described and formalized in this paper. The Fidalgo Complex and its sedimentary cover are the structurally highest rocks in the San Juan thrust system.The Fidalgo Complex is a highly disrupted Middle to Upper Jurassic ophiolite with arc-related intrusives, volcanics, and sediments. The Trump unit is an informally named sequence of siliceous sediments, volcanic graywacke, and minor volcanics that occurs at the stratigraphically highest portion of the Fidalgo Complex. Complex facies, lithologies, and provenance indicate that deposition of this Oxfordian(?) to upper Tithonian unit occurred in an arc-proximal setting.The upper Tithonian and younger Lummi Group (elevated here) lies depositionally above the Fidalgo Complex; locally the contact is an angular unconformity. The James Island Formation (new) is designated as a lower unit of the Lummi Group in the Decatur Island area. The chert-rich volcaniclastic sediments of the James Island Formation, locally containing ophiolitic debris, represent submarine-fan deposition within a tectonically active basin where basement blocks were uplifted along fault scarps.Middle Cretaceous thrusting and lawsonite–prehnite–aragonite metamorphism predated deposition of the Obstruction Formation (new), which is inferred to unconformably overlie the Lummi Group – Fidalgo Complex. Metamorphism postdated the late Albian, as rocks of this age are metamorphosed. The Obstruction Formation (?Cenomanian–Turonian) does not have metamorphic lawsonite–prehnite–aragonite, which are characteristic of underlying terranes in the San Juan Islands. Instead, the Obstruction Formation contains clasts derived from underlying metamorphosed terranes in the San Juan Islands; some clasts show these high-pressure, low-temperature metamorphic minerals. The Obstruction Formation probably represents synthrusting sedimentation that occurred after the San Juan terranes were metamorphosed and rapidly brought to the surface by continued thrusting over a hanging-wall obstruction. Thrusting was most likely driven by the accretion of Wrangellia against the North American margin.