ABSTRACTFive histone deacetylase genes (HDA1, RPD3, HOS1, HOS2,andHOS3) have been cloned fromCandida albicansand characterized. Sequence analysis and comparison with 17 additional deacetylases resulted in a phylogenetic tree composed of three major groups. Transcription of the deacetylasesHDA1andRPD3is down-regulated in the opaque phase of the white-opaque transition in strain WO-1.HOS3is selectively transcribed as a 2.5-kb transcript in the white phase and as a less-abundant 2.3-kb transcript in the opaque phase.HDA1andRPD3were independently deleted in strain WO-1, and both switching between the white and opaque phases and the downstream regulation of phase-specific genes were analyzed. Deletion ofHDA1resulted in an increase in the frequency of switching from the white phase to the opaque phase, but had no effect on the frequency of switching from the opaque phase to the white phase. Deletion ofRPD3resulted in an increase in the frequency of switching in both directions. Deletion ofHDA1resulted in reduced white-phase-specific expression of theEFG13.2-kb transcript,but had no significant effect on white-phase-specific expression ofWH11or opaque-phase-specific expression ofOP4, SAP1,andSAP3.Deletion ofRPD3resulted in reduced opaque-phase-specific expression ofOP4, SAP1,andSAP3and a slight reduction of white-phase-specific expression ofWH11and 3.2-kbEFG1. Deletion of neitherHDA1norRPD3affected the high level of white-phase expression and the low level of opaque-phase expression of the MADS box protein geneMCM1, which has been implicated in the regulation of opaque-phase-specific gene expression. In addition, there was no effect on the phase-regulated levels of expression of the other deacetylase genes. These results demonstrate that the two deacetylase genesHDA1andRPD3play distinct roles in the suppression of switching, that the two play distinct and selective roles in the regulation of phase-specific genes, and that the deacetylases are in turn regulated by switching.