The late Paleozoic “basement” rocks that crop out along the Pacific side of the Chonos Archipelago (44°–46°S) can be divided into two north‐south trending belts: (1) an eastern belt formed of submarine fan‐turbidites and subordinate pelagic cherts, each containing well‐preserved primary sedimentary structures, and (2) a western belt, mainly formed by strongly foliated mica schists and greenschists. Trace element contents in the cherts and greenschists indicate rocks of oceanic affinity. The structures present within the eastern rock suite are principally subiso‐clinal folds (with tectonic imbrication) and locally developed zones of broken formation. The transition from these rocks into the foliated schists appears to be related to a progressive increase in metamorphism and strain associated with the development of westward verging recumbent folds and a flat‐lying crenulation cleavage. It is inferred that these structures developed during the construction of a Late Carboniferous‐Early Permian accretionary prism (about 260 Ma Rb‐Sr ages), although sedimentation may have taken place throughout the upper Paleozoic. Rb‐Sr whole‐rock isochrons giving Late Jurassic to Early Cretaceous ages for some localities may indicate much later development of S2 structures. Alternatively, they may represent isotopic resetting by hydrothermal effects during the emplacement of transgressive Early Cretaceous granites, one of which gives a new Rb‐Sr isochron age of 125±2Ma. This overall scenario seems to be consistent with that reported in the slightly older coastal metamorphic basement north of 34°S and equivalent or younger complexes farther south in the Madre de Dios Archipelago.