We resurveyed an elevational transect in the Great Smoky Mountains National Park first sampled in 1947 for chromosomal polymorphisms in populations of Drosophila robusta. Combining these results with those from previous surveys, unpublished data, and long-term meteorological data from this region up to 2003, we found that these chromosomal polymorphisms had continued to shift in frequency consistent with long-term temperature changes, yet had maintained elevational clines. Intensity of linkage disequilibrium for X-chromosome gene arrangements had shifted up and down the transect over the 56-year sampling period, suggesting shifting patterns of adaptation. Chromosomal frequency changes through the 1980s clearly demonstrated concerted directional evolution in response to cooler temperatures, but over the 20 years until 2003, frequency changes in most high-elevation populations reversed for many of the most temperature-sensitive gene arrangements. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88, 131–141.