The grasshopper Chorthippus parallelus is genetically differentiated over its range into at least five major geographical subdivisions. Two of these subdivisions, designated as subspecies, meet and form a hybrid zone in the Pyrenees. These subspecies differ for a wide range of morphological, behavioural and chromosomal characters, which vary clinally across the zone. A further geographical subdivision exists within Italy. Here we present the first evidence for chromosomal divergence between populations of the grasshopper north and south of the Alps. Across two Alpine cols (Col de Larche, between France and Italy; Passo de Resia, between Austria and Italy), these populations differ in both structural and functional components of the X‐chromosome. Northern Alpine individuals possess an active nucleolar organizing region (NOR) at the distal end of the X‐chromosome and an associated region of heterochromatin (C‐band). Both these features are absent from individuals from the south of the Alps. However, all individuals examined carry distally located rDNA on the X‐chromosome. Clinal transition was examined in the distal C‐band in transects through the two cols. The cline centres are roughly coincident with the tops of the cols. Both clines were of similar widths (Col de Larche, 21.88 km; Passo de Resia, 24.05 km), and therefore much wider than those for an X‐linked distal C‐band in the Pyrenean hybrid zone. This suggests that there are different selective pressures on the cytogenetic characters in the Alps. The results are discussed in the context of the historical population dynamics of the species in relation to the climatic changes associated with the Pleistocene ice ages.