We examined the phylogeographic patterns of Paracalliope fluviatilis (Amphipoda) over its entire range and the prevalence of mate discrimination in laboratory mate choice tests using genetically distinct populations. We predicted that mate discrimination would increase as the level of genetic divergence increased between populations. Thirty different haplotypes were found with pairwise sequence divergences in the range 1–23.5% between locations. Individuals were selected from seven genetically distinct populations and males were presented with ‘local’ (same population) or ‘foreign’ (genetically divergent) females. Males were more likely to pair with local than foreign females but there was no evidence of a gradual increase in discrimination. Discrimination became most prominent (approximately 5 : 1 local : foreign) when genetic divergences exceeded approximately 20%; matings between divergent individuals also resulted in significantly fewer females producing eggs. We suggest that: (1) this abrupt shift in discrimination occurs because individuals from different, but similarly divergent, clades rely on different recognition cues (e.g. moulting pheromones with disparate chemical signatures) that trigger recognition and subsequent discrimination of incompatible mates; (2) geological history associated with sea level changes and a series of isolation events may be responsible for the patterns of discrimination that we observed; and (3) amphipods may be more genetically variable relative to other invertebrate taxa. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 196–205.