Lake Tanganyika is by far the oldest East African rift lake (Cohen et al. 1993). This lake harbours an extraordinary diversity of endemic organisms and its cichlid fauna is morphologically, ecologically and behaviorally the most diverse cichlid species flock of the African lakes (Fryer and Iles, 1972; Greenwood, 1984; Coulter 1991; Rossiter, 1995). As the result of rapidly increasing growth of the human population around the lake, its unique freshwater ecosystem is not only threatened by resource overexploitation such as the the depletion of its fish stocks by overfishing. In addition, Lake Tanganyika is also threatened by industrial and argicultural pollution (fertilizers, pesticides) and excessive amounts of sedimentation in the lakecaused by deforestation (Cohen 1992). As the result of these environmental changes, water quality may soon deteriorated to such a degree that threatens the survival of the unique endemic fish- and invertebrate species flocks of Lake Tanganyika, particularly along its extremely species rich rock bottom habitats. Recent studies have shown that our taxonomical knowledge of the Tanganyikan cichlid fauna is less advanced than often assumed (Snoeks et al. 1994). This is important since it is evident that in order to evaluate the effects of environmental changes on the species communities in the littoral habitats of Lake Tanganyika, a sound taxonomical knowledge on these complex species assemblages is required. However, to date, we still ignore many important facts about these species communities; for example, many species are only described on the basis of very few specimes - usually from only one or two localities, and it becomes more and more evident that an unknown number of have yet to be discovered and named. The pertinent lack of fundamental knowledge about this fauna raises critical questions such as (1)?how much do we really know about the biodiversity in Lake Tanganyika?? and (2) ?what measures should be taken to conserve the unique fauna of this lake??. It is our objective population level mtDNA and microsattelite studies on a small selection of rock-dwelling Tanganyikan cichlid fishes also yield relevant knowledge concerning the true nature of the biodiversity that should be the concern of anyone who wishes to conserve this unique but endangered fauna.