The Cks or Suc1 proteins are highly conserved small proteins that play remarkably diverse roles in the cell cycle. All Cks homologues have the ability to associate with Cyclin dependent kinases (Cdks) and in many cases this interaction has been shown to be important for function. Here we characterize the null and RNAi knockdown phenotype of the Drosophila Cks1 (Cks85A) gene. Cks85A is essential for viability in Drosophila. Cks85A null animals have reduced overall growth and this correlates with reduced ploidy and impaired DNA replication in endoreplicating cells. Interestingly, Cks85A is also required for the maintenance of diploidy in mitotically cycling cells. The requirement for Cks85A in growth is similar to that of the mammalian Cks1, which was found to interact with the SCF(Skp2) ubiquitin ligase. We identified the Drosophila Skp2 gene and generated null alleles. Comparison of these mutants to null mutants for Cks85A reveals a remarkably similar dual requirement in growth and in maintenance of diploidy. We find that Cks85A interacts directly with the SCF(Skp2) ubiquitin ligase and genetic evidence indicates that this is its major molecular function. The closely related Cks30A cannot interact with the SCF(Skp2) and cannot functionally compensate for loss of Cks85A. We also find that the critical growth promoting and diploidy maintaining functions of Cks85A and Skp2 are independent of known SCF(Skp2) substrates, p27 and Cdt1, indicating that other critical substrates remain to be identified.