Collembola take an exceptional and fascinating position in the tree of life. Together with other basal hexapods (e.g. Protura, Diplura) they are positioned in-between the insects and crustaceans. However, recently some authors suggested that the six-legged body plan found among basal hexapods and insects evolved minimally twice (e.g. [46, 47]). The dataset presented here might add the sequence information that is needed to gain a more detailed insight into the evolution of these groups, and the relationship between insects and crustaceans. Using the BLAST tool, Collembase can be queried for genes valuable for phylogenetic inference. Degenerate PCR primers can be developed on the retrieved sequences to obtain information on other basal hexapod groups.