Research to date on the relationship between climate change and agriculture has focused primarily on annual crops. Long-term perennial crops such as apple trees give researchers the opportunity to study a more longitudinal record of human-climate interactions. In Appalachia, one of the earliest orchard areas in the United States, many orchards have been run by single families for multiple generations, and oral histories contain climate information stretching back several decades or longer. We investigated folk crop varietal diversity in southern Appalachian orchards, grower observations and perceptions of environmental change, and the potential effects of climate change on apple diversity. Twenty-two orchardists were consulted in Appalachian North Carolina, using a combination of participant observation, free-listing exercises, in-depth semi-structured interviews, and benchmark socioeconomic surveys. We documented 450 apple ethnotaxa in 22 orchards. Our results show that although a majority of growers recognize increased climate variation and variability in annual and seasonal weather patterns, only a minority attribute those changes to human activity. The major environmental change of concern to orchardists in the study region is warmer winters and earlier springs, which can cause devastating losses to apple production. Current consumer and market trends are selecting away from diverse and potentially disease- and weather-resistant heirloom apple varieties toward modern commercial varieties that are highly susceptible to environmental change. Apple diversity is threatened in southern Appalachia as a result of multiple factors, yet maintaining high diversity levels may be a key adaptive strategy in the face of global climate change.