Seismic data reveal that water level in Lake Malawi, East Africa, was 250 to 500 meters lower before about 25,000 years ago. Water levels in Lake Tanganyika at that time were more than 600 meters below the current lake level. A drier climate appears to have caused these low stands, but tectonic tilting may also have been a contributing factor in Lake Malawi. High-angle discordances associated with shallow sequence boundaries suggest that these low stands probably lasted many tens of thousands of years. Because of its basement topography, the Lake Tanganyika basin had three separate paleolakes, whereas the Lake Malawi basin had only one. The different geographies of these paleolakes may be responsible in part for the differences in the endemic fish populations in these lakes.