Phylogenetic relationships of 19 species representing nine holometabolous insect orders and three outgroup orders were examined using sequence data from two-thirds of the 18S nuclear ribosomal RNA molecule. Of 1330 aligned nucleotide sites in 19 taxa, 460 were variable and used for phylogenetic analysis. Parsimony analyses resolved relationships in a few groups but left the most controversial questions regarding relationships among major lineages unresolved. All analyses supported a clade with Lepidoptera and Trichoptera as sister taxa most closely related to Diptera. Mecoptera and Siphonaptera were most often linked basally to this group, supporting the existence of the Mecopterida superorder. Phylogenetic affinities of this superorder and remaining lineages, Coleoptera, Hymenoptera, and neuropterids, were ambiguous. In contrast, distance analysis produced a tree supporting one of three morphologically based hypotheses. Neuroptera and Hymenoptera were placed as sister taxa ancestral to Mecopterida, with Coleoptera basal to all orders. The inability of the 18S molecule to resolve ancient divergence events may be due to the rapid divergence of holometabolous orders, resulting in few synapomorphies.