The fresh and saline lakes of Ounianga Kebir and Serir in northeastern Chad are among the very few permanent aquatic ecosystems currently existing in the hyper-arid core of the Sahara desert. The confirmed modern fauna of aquatic molluscs at Ounianga comprises three widespread species (Melanoides tuberculata, Biomphalaria pfeifferi and Lymnaea natalensis), of which only the first appears to maintain a thriving population. We recovered seven more species of gastropods, among which one is new to science (Gabbiella ouniangaensis), and one bivalve species from early Holocene outcrops of diatomaceous limestone at Ounianga Serir. All species except one are known to be commonly spread between lake and river systems by birds, and in its entirety this species-rich fossil mollusc fauna of Ounianga Serir resembles that of other Saharan lake sites known to have been hydrologically isolated during the early Holocene. The impoverished modern mollusc fauna, which lacks even the widespread and opportunistic species Bulinus truncatus, may have become established relatively recently through new colonisation events, following eradication of the early Holocene mollusc fauna during a later episode of high salinity or desiccation. Copyright © 2011 John Wiley & Sons, Ltd.