Significant advancements in understanding the complex evolution of the Tofino Basin at a convergent accretionary margin are enabled by combining contextual geologic information with new isotopic and paleontological data. A high-resolution Cenozoic chronostratigraphy of the basin is constrained by strontium isotope ages (36.9–1.3 Ma) of Late Eocene to Pleistocene foraminifers together with a revised biostratigraphy (foraminifers and ichthyoliths) from six offshore wells and outcrop samples, new specimen thermal alteration values, and existing well log data. These data are integrated with archival multichannel seismic and magnetic data to interpret offshore well positions with relation to sub-basins and structural highs of the Pacific Rim and Crescent terranes, and other accreted strata. Six regions of the Tofino Basin are defined based on structure and depositional differences during the Eocene to Holocene history of accretion and fragmentation of the Crescent terrane and it underthrusting the Pacific Rim terrane. Subsequent oceanic sediment accretions and deposition of overlying sediments up to about 4000 m thick resulted as the Juan de Fuca plate subducted beneath Vancouver Island. Observations include different fragmentations and landward movements of the Crescent and Pacific Rim terranes in the regions and two fault styles in the Ucluelet and Carmanah regions where six new sub-basins are defined. Results, especially for the Ucluelet and Carmanah sub-basins, indicate periods of deformation during the Late Eocene, Late Oligocene, Middle–Late Miocene, and post middle Pliocene, whereas the Early Oligocene and Early Miocene had periods of relatively slow and less disturbed deposition.