High-resolution shallow seismic reflection (Uniboom) and echosounding profiles obtained on the shelf and upper slope areas of Anamur Bay (Turkey, northeastern Mediterranean) were studied together with previous data on the onshore geology of the area to investigate the origin and related seismic stratigraphy of the submarine Anamur Canyon. It was found that the main axial trend of the submarine Anamur Canyon is aligned with the offshore projection of the N-S orientated, onshore Anamur thrust fault of Late Cretaceous (Senonian) to Early Tertiary age. Interpretation of the distinct reflection configurations observed on the seismic profiles reveals the presence of various seismic facies comparable with the depositional sequences resulting from the relative sea-level changes during the Late Quaternary. The acoustic basement (probably Miocene in age) is overlain by a sedimentary column (mainly Plio-Quaternary) which, in turn, can be divided into two major seismic sequences and 12 seismic facies that show considerable variations in both their lateral and horizontal extent. A palaeo-deltaic environment (Sequence 1), with its typical topset and foreset facies, was recognized and the corresponding deposits are interpreted to be indications of coastal deltaic progradation during Late Pleistocene sea-level highstands, or during the early phases of the last major eustatic lowering. Reflections of Sequence II, which includes nine distinct facies, are marked by onlap configuration and are believed to be marine deposits of the Flandrian transgression. At least four transgressive cycles are evident from the seismic profiles, at 70-90, 60, 45 and 40 m water depths. The two sequences (I and II) are now covered with the most recent facies.