Melkhoutboom Cave is an archaeological site dating to the Later Stone Age, located in the Zuurberg Mountains, Cape Folded Mountain Belt, Sarah Baartman District Municipality in the Eastern Cape Province of South Africa.

Melkhoutboom Cave was first excavated in 1930 by John Hewitt, whose findings prompted it to be included in the Albany Museum's “Prehistory of the Eastern Cape” project, initiated in 1963.[3] Excavations took place at the cave as part of this project in 1967 and 1969. The initial small-scale excavation of a 3 m × 1 m (9.8 ft × 3.3 ft) test pit in 1967 was conducted to confirm and clarify the findings from Hewitt's original excavation in the early 1930s. The subsequent excavation in 1969 was planned based on this initial excavation, extending and building upon it. Both excavations used the same grid system running north–south and east–west.

Of the approximately 150 square meters of “living area” inside the cave, about a fifth has been excavated, and only half of that area has been excavated all the way down to bedrock. This was primarily due to constraints on time and resources, which stopped excavation from being extended to promising areas or even bringing the whole of the excavated area down to bedrock; instead, efforts were focused on obtaining a large sample of artifacts and floral and faunal remains from the area already excavated.

The excavated area of Melkhoutboom Cave was divided into stratigraphic units based on soil composition and cultural content. The names given to these units and their estimated ages based on radiocarbon dates of hearths or artifacts are as follows, from bedrock to the surface: Basal Unit (15,400 years BP), Rock Fall Unit (10,500 years BP), Medium Brown Series Unit (7,660 years BP), Wilton Base Marker Unit (7,300 years BP), Marker Unit (indirectly dated by comparison to preceding and overlying units), Wedge Unit (6,980 years BP), Main Bedding Unit (5,900 years BP), Cut Away Frontal Unit (2,870 years BP), the Overlie of the Main Bedding Unit, and the Surface Unit. The Wilton Base Marker Unit in particular appears to represent a major technological break from underlying units based on the cultural material found.