Hox genes are evolutionarily conserved transcription factors that regulate the expression of other developmental genes. They are organized into clusters, with the order of genes in each cluster paralleling their expression along the anterior-posterior axis. In the free-living nematode Caenorhabditis elegans, the Hox genes are much more dispersed along the chromosome, and the anterior Hox genes,
ceh-13 and
lin-39, are reversed, but little is known about the Hox genes in other nematode taxa. We are interested in the Hox gene cluster architecture of insect parasitic nematodes from the genus Steinernema (S. carpocapsae, S. scapterisci, S. feltiae, S. glaseri, and S. monticolum), for which we have assembled genomes and stage-specific transcriptomes. More specifically, we are interested in exploring the presence, order, and dispersal of the Hox genes in these newly sequenced nematodes, to identify the level of conservation within this genus and their conservation with C. elegans. We also investigated the extent of non-coding conservation around Hox genes, looking for candidate regulatory regions. Surprisingly, the Hox gene cluster among steinernematids is very different from what is known in C. elegans. For example, we have found approximately 10 genes between the steinernematid Hox genes
ceh-13 and
lin-39, whereas the region between the orthologous
ceh-13 and
lin-39 Hox genes in C. elegans is a gene desert. Interestingly, many of the intervening genes in the steinernematids are conserved and expressed in C. elegans, but are located nowhere near the C. elegans Hox cluster. We explored this in another nematode genome that we have assembled, Panagrellus redivivus, where we find only two intervening genes present between
ceh-13 and
lin-39 Hox genes. These findings suggest that the organization of the Hox cluster in nematodes has structural plasticity and varies across the phylum.