In the budding yeast S. cerevisiae, Swe1 delays the onset of mitosis by phosphorylation and inactivation of the cyclin-dependent kinase Cdc28, thereby relaying the morphogenetic signal to the cell cycle. Hsl1/Nik1, Kcc4 and Gin4 are structurally homologous protein kinases that localize to the bud neck and negatively regulate Swe1 by phosphorylation. We report here that Kcc4 and Gin4 have partially overlapping but essentially distinct cellular functions. Deletion of KCC4 had a similar effect to GIN4 deletion, causing moderate defects in bud formation at stationary phase; overexpression of Kcc4 inhibited cell growth. KCC4 showed functional interaction with GIN4 in cdc28 mutants, and both Kcc4 and Gin4 proteins physically interacted with Swe1 in vitro. However, unlike gin4Δ cells, kcc4Δ cells were not elongated but multi-budded at stationary phase, and showed resistance to 0.04% SDS and 0.003% calcofluor white. In light of the observation that Kcc4 and Gin4 specifically associate with distinct septin proteins, we propose that the observed functional distinction between Kcc4 and Gin4 is due to differences in septin association partners.