Little is known about the life histories, genetic structure, and population connectivity of shallow groundwater organisms. We used next-generation sequencing (RAD-seq) to analyze population genomic structure in two aquifer species: Paraperla frontalis (Banks, 1902), a stonefly with groundwater larvae and aerial (winged) adults, and Stygobromus sp., a groundwater-obligate amphipod. We found similar genetic differentiation in each species between floodplains separated by ~70 river km in the Flathead River basin of NW Montana, USA. Given that Stygobromus lacks the aboveground life stage of P. frontalis, our findings suggest that connectivity and magnitude of genetic structure cannot be definitively assumed from life history differences.