The segmentation gene hierarchy of Drosophila melanogaster represents one of the best understood of the gene networks that generate pattern during embryogenesis. Some components of this network are ancient, while other parts of the network have evolved within the higher Diptera. To further understand the evolution of this gene network, we are studying the role of gap genes in a representative of a basally diverging dipteran lineage, the moth midge Clogmia albipunctata. We have isolated orthologues of all of the Drosophila trunk gap genes from Clogmia, and determined their domains of expression during the blastoderm stage of development, in relation to one another, and in relation to the expression of even-skipped (Calb-eve), a component of the pair-rule system that is directly regulated by the gap genes in Drosophila. We find that hunchback (Calb-hb), Krüppel (Calb-Kr), knirps (Calb-knl), giant (Calb-gt) and tailless (Calb-tll) are all expressed in patterns consistent with a gap segmentation role during blastoderm formation, but huckebein (Calb-hkb) is not. In the anterior half of the embryo, the relative positions of the gap gene expression domains in relation to one another, and in relation to the eve stripes, are rather well conserved. In the posterior half of the embryo, there are significant differences. Posteriorly, Calb-gt is expressed only transiently and very weakly, in a domain that overlaps entirely with that of Calb-knl. At late blastoderm stages, none of the candidate genes we have tested is expressed in the region between the posterior Calb-knl domain and Calb-tll. It is likely that the regulation of Calb-eve expression in this posterior region depends on combinations of gap gene factors that differ from those utilised for the same stripes in Drosophila. Both the gap and the pair-rule patterns of gene expression are dynamic in Clogmia, as they are in Drosophila, shifting anteriorly as blastoderm development proceeds.