Mitochondrial DNA sequence analysis was used to investigate genetic diversity and phylogeographic population structure among geographically isolated alpine populations of the amphipod Gammarus fossarum. This study was performed across a region with an important glacial history and substantial geographical variations in calcium levels, in order to evaluate the relative impact on the genetic diversity of the population history and this environmental factor known to be associated with local adaptation and population growth. Analysis of the nucleotide sequences for a 376-bp segment of the cytochrome c oxidase I gene in 84 specimens from seven different populations revealed 20 different haplotypes distributed into five major lineages that are not geographically structured. Analysis of molecular variance indicates that the populations from the crystalline massif are less diverse than those living on limestone, suggesting a global correlation between genetic diversity and calcium concentration of the water. However, the role of this environmental factor appears to be indirect, with smaller population size leading to lower genetic diversity.