Phylogeographic analyses of the genus Eremophila (Horned Lark E. alpestris and Temminck’s Lark E. bilopha) were carried out based on the mitochondrial cytochrome b and ND2 genes. Four primary lineages with para-/allopatric distributions were identified: (1) a Qinghai–Tibetan–Himalayan lineage; (2) a North African and Middle Eastern lineage; (3) a northwest African and southeast European/southwest Asian lineage; and (4) a Northern Palearctic and North American lineage. The relationships between these four lineages were poorly resolved. They were estimated to have diverged in the late Pliocene to early Pleistocene, although the dates are uncertain due to topological ambiguity and wide confidence intervals. The sublineages were estimated to have diverged around the Middle Pleistocene (c. 0.8–0.2 mya). A strong signal of population growth and range expansion was observed from the Middle Pleistocene, at least in the North Palearctic subclade (A2). Morphometric analysis of the Eurasian taxa revealed a high degree of overlap among taxa, although E. bilopha and E. a. longirostris stood out from the others. We support a recent suggestion to split E. alpestris into multiple species, although we propose four instead of six species, corresponding to the four primary lineages identified in this study: (1) Himalayan Horned Lark E. longirostris (by priority and on the premise that the genetically unsampled taxon longirostris belongs to this clade); (2) Temminck’s Lark E. bilopha; (3) Mountain Horned Lark E. penicillata; and (4) Common Horned Lark E. alpestris (sensu stricto). Our results illustrate the discrepancy between phylogenetic relationships and phenotype in larks.

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