The possibility of gene tree incongruence in a species-level phylogenetic analysis of the genus Ips (Coleoptera: Scolytidae) was investigated based on mitochondrial 16S rRNA and nuclear Elongation factor-1α sequences, and existing Cytochrome Oxidase I and non-molecular data sets. Separate cladistic analyses of the data partitions resulted in partially discordant most-parsimonious trees but revealed only low conflict of the phylogenetic signal. Interactions among data partitions, which differed in the level of sequence divergence (COI > 16S > EF-1α), base composition, and homoplasy, revealed that much of the branch support only emerges in the simultaneous analysis, in particular for deeper nodes in the tree which are almost entirely supported due to "hidden support" (sensu Gatesy et al., 1999). Apparent incongruence between data partitions is in part due to suboptimal alignments and bias of character transformations, but there is little evidence to invoke incongruent phylogenetic histories of genetic loci. There is also no justification for eliminating or downweighting gene partitions based on their level of homoplasy or apparent incongruence with other partitions, as the signal only emerges in the interaction of all data. In comparison to the traditional taxonomy, the pini, plastographus and perturbatus groups are polyphyletic, whereas the grandicollis group is monophyletic except for the inclusion of the (monophyletic) calligraphus group. The latidens group and some European species are distantly related and closer to other genera within Ipini. Our robust cladogram was used to revise the classification of Ips. We provide new diagnoses for Ips and four subgeneric taxa.