Cullins confer substrate specificity to E3-ligases which are multi-protein complexes involved in ubiquitin-mediated protein degradation or modification. There are six cullin genes in Drosophila melanogaster. We have raised an antibody against Cul-5 and demonstrated that it expresses in neuronal and non-neuronal cells throughout development. In the embryonic tracheal system, Cul-5 is enriched at fusion sites together with E-Cadherin and Fasciclin III. Mutations of cul-5 do not affect tracheal development but do show defects in the organization of synaptic boutons at the larval neuromuscular junction where the protein is expressed in a subset of motoneuron terminals. Loss of function of another cullin gene ‘cul-2’ results in similar defects at the larval neuromuscular junction although cul-2;cul-5 double mutants do not show an enhanced phenotype. Both cul-2 and cul-5 mutants show similar aberrations in the development of female germ line. Our results suggest that both of these cullin proteins participate in similar developmental processes.