Humans are modifying our planet’s ecosystems with increasing frequency and intensity. Exploring population responses to anthropogenic modifications of natural habitat provides insights into how species persist in the Anthropocene. Here, we leverage natural history collections to document rapid phenotypic change within a native bird population following 80 years of agriculture in the Colorado Desert of southeastern California. By comparing spectrophotometric measurements of Horned Lark (Eremophila alpestris) specimens collected in the Imperial Valley from 1918 to 1934 to those collected from 1984 to 2014, we found that more recent birds have darker backs, napes, and crowns. This dorsal darkening may have resulted from a shift in selective pressures for camouflage induced by land use: previously, the lark population nested on light-colored desert flats, whereas contemporary larks occupy darker soil associated with agricultural fields. Adaptation and/or introgression may have contributed to this instance of rapid phenotypic change following the rise of agriculture in the Imperial Valley.