The amphipod diversity in the Siberian Lake Baikal is unique, with some 260 endemic species and 80 additional subspecies recognized so far. Three general patterns of differentiation in molecular data, however, suggest that this is still a gross underestimate of the actual number of species. Firstly, allozyme analyses regularly indicate a species-level distinction for taxa previously treated as subspecies there corroborated for Micruropus talitroides,l eurypus, M. wahlii / platycercus and Eulimnogammarus verrucosus / oligacanthus). Secondly, so far unrecognized (sibling) species are detected even sympatrically (e.g., in both the Micruropus complexes above). Thirdly,'conspecific' samples from different parts of the lake, of several Pallasea spp., regularly show diagnostic allozyme differences suggesting presence of vicariant sibling. species in the main geological subdivisions of the basin. Extrapolating the observations to the whole of the Baikalian amphipod fauna, a reasonable projection for the total number may be close to a thousand species. Molecular data suggest that the conventional Baikalian lineages are remarkably old, whereas the vicariant new taxa may have arisen recently in the (early) Pleistocene. These dual levels of diversity are paradoxical in view of the lake's history and the forces supposed to underlie the diversification and speciation processes. The well defined and specialized forms originated in times when the climate and environments were grossly different from the present: not as a response to the present kind of environments. On the other hand, the divergence that has arisen within the time frame of the environmentally modern Lake Baikal (a single basin and cool climate, < 2-3 Myr) appears to be related to geography rather than to adaptive features of morphology and ecology. The patterns prompt a reconsideration of the role of geographical isolation in recent speciation within Lake Baikal.