Bell’s and Sagebrush sparrows (Artemisiospiza belli and A. nevadensis) are phenotypically and genetically distinct, but data have yielded contradictory findings for A. belli subspecies. Disjunct populations of A. b. canescens from the San Joaquin Valley and Mojave Desert are phenotypically indistinguishable but diagnosable from Coast Range A. b. belli. However, San Joaquin Valley A. b. canescens shares allozymes and mtDNA with A. b. belli whereas Mojave Desert A. b. canescens is genetically distinct. Furthermore, Great Basin A. nevadensis is closer in mtDNA to non-desert A. belli subspecies than to Mojave Desert A. b. canescens, with whom it contacts across an aridland transition. We assessed concordance of song with genetics and phenotype for these taxa, and also analyzed songs and mtDNA for A. b. clementeae which is endemic to arid San Clemente Island off the coast of southern California. Songs of open, arid habitat populations (A. nevadensis, A. b. canescens, A. b. clementeae) are consistently more similar to each other than they are to songs of coastal A. b. belli. We examined bioclimatic and land cover conditions to understand the basis for these patterns across ecoregions, and discuss the effect of the acoustic environment on song.