Late Carboniferous to Permian strata of the Lower Karoo sequence in the Kalahari Karoo Basin, Botswana, contains suitably preserved palynomorphs for biostratigraphic classifications. All taxa described from eight out of the nine coreholes sampled for the study comprise sixty-eight genera made of one hundred and sixty-five miospore species, eleven arcritarchs species, seven prasinophytes species, and 1 chlorophyte species. Two wellsampled coreholes, namely STRAT 1 and CKP6, have lacial facies, to warm and drier conditions during deposition of the lower Ecca sequences. Palaeoclimatic conditions ultimately turned wet during middle Ecca times generating coal-forming settings. Palaeoenvironmental interpretations based on palynofacies data indicate a predominantly proximal palaeo-depositional setting for the entire Lower Karoo sequence at STRAT 1 borehole. The broader depositional environment transformed from glacial sub-environments, during deposition of the Dwyka Group, into a relatively wider basin punctuated by some rare marine incursions, in the early Ecca Group, and ultimately developing into a deltaic system.