This paper presents new information obtained from a recent excavation and reassessment of the stratigraphy, chronology, archaeological assemblages and environmental context of the Apollo 11 rockshelter, which contains the longest late Pleistocene and Holocene archaeological sequence in Namibia. The Middle Stone Age (MSA) industries represented at the site include an early MSA, Still Bay, Howieson’s Poort and late MSA. Optically stimulated luminescence (OSL) dating of individual quartz grains yielded numerical ages for the Still Bay and Howieson’s Poort, and indicated the presence of a post-Howieson’s Poort phase. OSL dating also verified conventional and accelerator mass spectrometry radiocarbon ages for a further two later MSA phases. The timing of the transition from the MSA to the early Later Stone Age was also investigated. Improved resolution of the excavation and a more detailed stratigraphy revealed the presence of near-sterile cultural layers, which in some cases assisted in subdividing the MSA cultural phases. Such information, in combination with the new radiocarbon and OSL chronologies, helps address questions about the duration and continuity of MSA occupation at the site. Analyses of the faunal and archaeobotanical remains show some differences between the occupation phases at the site that may be associated with changing environmental conditions.