We studied morphology (shell, penis and flagellum, female reproductive organs) and 395 partial sequences of mtDNA COI and 93 of ITS-1 in Bythinella from continental Greece. Molecular techniques inferred ten molecularly distinct species: two in the Peloponnese; one in the Parnassus and Attica; two sympatric/parapatric at Volos; one in the Lefkas; four in northern Greece. The differentiation was probably not older than 3.5 MYA, most species originated in the last 2 MYA (Pleistocene). Haplotype diversity, nucleotide diversity and mismatch distribution indicated common bottlenecks followed by fluctuations in population size. A nested-clade analysis indicated allopatric fragmentation with instances of long distance colonization, and restricted gene flow with isolation by distance. The decrease in Bythinella species richness from the north to the south was due to the geological history, colonization and recolonization, and short and long-distance dispersal, to survive in the unstable environment.