Abstract. In terminal Pliocene–early Pleistocene times, part of the Malawi Basin was occupied by paleo-lake Chiwondo. Molluscan biostratigraphy situates this freshwater lake either in the East African wet phase between 2.7–2.4 Ma or that of 2.0–1.8 Ma. In-lake divergent evolution remained restricted to a few molluscan taxa and was very modest. The lacustrine Chiwondo fauna went extinct at the beginning of the Pleistocene. The modern Lake Malawi malacofauna is depauperate and descends from ubiquistic southeast African taxa and some Malawi basin endemics that invaded the present lake after the Late Pleistocene mega-droughts. The Pleistocene aridity crises caused dramatic changes, affecting the malacofauna of all East African lakes. All lacustrine endemic faunas that had evolved in the Pliocene rift lakes, such as paleo-lake Chiwondo, became extinct. In Lake Tanganyika, the freshwater ecosystem did not crash as in other lakes, but the environmental changes were sufficiently important to trigger a vast radiation. All African endemic lacustrine molluscan clades that are the result of in-lake divergence are hence geologically young, including the vast Lavigeria clade in Lake Tanganyika (ca. 43 species).