The Late Triassic to Early Jurassic Molteno, Elliot and Clarens formations of the uppermost part of the Karoo Supergroup in the main Karoo Basin of South Africa form a distinct tectono-sedimentary sequence. A major problem with the modeling of this part of the Karoo basinal fill is that the nature of the Molteno-Elliot contact is poorly understood. Previously the contact has been defined on a mix of lithological and palaeontological criteria, and has been considered to be gradational or transitional in nature, with the Elliot considered the distal equivalent of the upper Molteno Formation. Recent field investigations demonstrate that the boundary can be defined on lithologic changes, including the gross and internal geometries of the sandstone units and contained lithofacies associations, the presence/absence of coal seams and paleosols, and on palaeocurrent patterns, sandstone composition and grain-size variations. This boundary represents a regional unconformity throughout the basin and the recognition of this cryptic second order sequence boundary invalidates previous interpretations of an interfingering stratigraphic relationship between the two formations. Stacking patterns in the upper Karoo Supergroup, and the tectonic framework of their development, suggest that the southern margin of the Kaapvaal Craton acted as a regional control on sequence development during Late Triassic - Early Jurassic times.