Understanding the population dynamics of a montane/alpine grasshopper species with a disjunct distribution may help to clarify the evolutionary mechanisms of the genus Melanoplus during the Pleistocene era. A total of 215 individuals of one such species, Melanoplus alpinus Scudder, was collected from 43 meadows (5 individuals per meadow) in 10 drainages of four mountain ranges in Wyoming and Montana. This sample structure allows for genetic analysis at four spatial scales: among mountain ranges, among drainages within ranges, among meadows within drainages, and within meadows. We examined whether genetic structuring differed among the sampling scales analyzed and whether present isolation between populations of M. alpinus reflects similar historical isolation. Polymerase chain reaction restriction fragment-length polymorphism analyses were conducted on two mtDNA regions (COI and COII), revealing nine haplotypes among the 215 individuals. DNA sequence analysis of 496 bp of the COI region for 23 individuals representing the various restriction fragment-length polymorphism haplotypes and ranges revealed three major lineages, with divergence rates that have been typically observed between species of Melanoplus. The three lineages may represent three cryptic species or a relatively ancient paraphyly in a single species. Regardless of which of these scenarios is true, analysis of molecular variance suggested that “M. alpinus” was a widely distributed, panmictic species at the end of the last Pleistocene glaciation that has since retreated to montane/alpine meadows of the central and northern Rocky Mountains. The presently fragmented distribution of the species is not indicative of historically similar isolation. The degree of genetic differentiation varied among geographical scales, being greatest among drainages and meadows within mountain ranges. Very little genetic differentiation existed among mountain ranges.