The bark beetle, Ips confusus (LeConte), provides an opportunity to study the influence of past geologic events and host use on lineage diversification of a herbivorous insect. This beetle mainly feeds on two pinyon pine (Pinus) species, but it has been collected from other conifer species. Isolation by host may contribute to lineage diversity and population structure. Alternatively, the repeat fragmentation of pine and beetle populations during the Pleistocene may explain population structure. We performed cladistic and nested clade analyses of mitochondrial DNA cytochrome oxidase I (mtDNA COI) sequence data from 95 I. confusus individuals collected from two hosts, P. monophyllae and P. edulis, and an atypical host, spruce (Picea pungens), from 10 western United States populations. Thirty-one most-parsimonious trees of 15 COI haplotypes demonstrated little association between host species and monophyletic groups. Thus, host use does not appear to contribute to genetic structure among populations. Nested clade analysis revealed three main haplotype lineages, each associated with eastern, southwestern, and western geographic localities. Estimation of the time to the most recent common ancestor places the start of lineage divergence during the Pleistocene (≈836,000 yr ago). Past glaciation events better explain genetic population structure among I. confusus populations.