An increasing number of cellular activities are under the regulation of lysine acetylation. This post-translational modification (PTM) is reversibly catalyzed by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Targeting these enzymes to different cellular compartments is instrumental in defining their substrates and functions in vivo. Here we showed that a S. cerevisiae HDAC Hos3 is asymmetrically targeted to the daughter side of the bud neck and to the daughter spindle pole body (SPB). Screening for mutants defective in targeting Hos3 to the bud neck identified septins and members of the morphogenesis checkpoint, pinpointing Hsl7 as the protein that recruits Hos3 to the bud neck. When spindle orientation defect is present, Hos3 is loaded symmetrically onto both SPBs. Importantly, although the neck localization of Hos3 is dispensable for a number of cellular activities, it is required for the response of Hos3 to spindle misorientation. When symmetrically associated with both SPBs, Hos3 may function as a spindle position checkpoint (SPOC) component to inhibit mitotic exit. The results together reveal how a uniquely targeted HDAC Hos3 functions as crosslink between the morphogenesis checkpoint and the SPOC. On a more general perspective, this study substantiates an important role of lysine acetylation in monitoring spindle orientation and regulating the cell cycle.