Cryptic species, i.e. species that are morphologically hard to distinguish, have been detected repeatedly in various taxa and
ecosystems. In order to evaluate the importance of this finding, we have to know in how far cryptic species differ in various
aspects of their biology. The amphipod Gammarus fossarum is a key invertebrate in freshwater streams and contains several
cryptic species. We examined the population genetic structure, genetic diversity and demographic history of two of them
(type A and type B) using microsatellite markers and asked whether they show significant differences. We present results of
population genetic analyses based on a total of 37 populations from the headwaters of two major European drainages,
Rhine and Rhone. We found that, in both species, genetic diversity was geographically structured among and within
drainages. For type A in the Rhine and type B in the Rhone, we detected significant patterns of isolation by distance. The
increase of genetic differentiation with geographical distance, however, was much higher in type A than in type B. This
result indicates substantial interspecific differences in population history and/or the extent of current gene flow between
populations. In the Rhine, type B does not show evidence of isolation by distance, and population differentiation is relatively
low across hundreds of kilometres. The majority of these populations also show signatures of recent bottlenecks. These
patterns are consistent with a recent expansion of type B into the Rhine drainage. In summary, our results suggest
considerable and previously unrecognized interspecific differences in the genetic structure of these cryptic keystone
species.