Calaphidinae is one of the most species rich group in Aphididae. However their phylogenetic relationship is poorly understood. In this study, we reconstructed phylogenetic relationship of Calaphidinae and closely related groups to confirm the taxon boundary and ingroup relationship such as tribe and genera. In addition, evolutionary hypothesis of ancestral host-plant relationship was tested. We performed Bayesian inference and maximum likelihood analyses of combined 4 mitochondrial (ATP6, COI, COII, CytB) and 1 nuclear (EF1α) sequences. Phylogenetic results suggested that Calaphidinae is not a monophyletic and Saltusaphidinae is nested in Calaphidinae. Phyllaphidinae forms a basal clade as the most primitive group of Calaphidinae. Reconstruction of ancestral host plant of Calaphidinae indicated that Calaphidinae might have evolved on members of Fagales plants.