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Lice are obligate parasites of mammals and birds and have become an important model for studies of host-parasite co-evolution and co-phylogenetics. Population genetic and phylogeographic studies represent an important bridge between microevolution and co-phylogenetic patterns. We examine co-phylogeographic patterns in sika deer and their parasitic lice. Co-phylogeographic patterns in deer and lice were evaluated using homologous regions of mitochondrial COI sequences. The phylogeographic breaks recovered for deer populations matched those of previous studies. Comparisons of the phylogeographic tree topology for deer lice with that of their hosts revealed a significant level of congruence. However, comparisons of genetic distances between deer and lice suggested that one of the estimated co-divergence events is more likely a recent host switch. Taking into account genetic divergence, there is not strong evidence for complete phylogeographic co-divergence between deer and their parasitic lice. However, mitochondrial phylogenies only track genetic structure of female lineages, and the incongruence between deer and louse phylogeography may be explained by louse migration mediated by male deer. Morphological analysis of head shape variation based on an elliptic Fourier descriptor showed that overall morphological variation contained phylogenetic signal, suggesting that in general morphology of these lice evolves congruent to population history.