Abstract: The SANT domain is a nucleosome recognition module found in transcriptional regulatory proteins, including chromatin modifying enzymes. It shows high functional degeneracy between species, varying in sequence and copy number. Here we investigate functions in vivo associated with two SANT motifs, SANT and SLIDE, in the yeast S. cerevisiae Isw1 chromatin remodeling ATPase. We show that differences in the primary structure of the SANT and SLIDE domains in yeast and D. melanogaster reflect their different functions. In yeast, the SLIDE domain required for histone interactions while this is a function of the SANT domain in flies. In yeast, both motifs are required for optimal association with chromatin and to form the Isw1b complex (Isw1, Ioc2, Ioc4). Moreover, nucleosome remodeling at MET16 is defective in strains lacking the SANT or SLIDE domains. In contrast, the SANT domain is dispensable for the interaction between Isw1 and Ioc3 in the Isw1a complex. We show that, although defective in nucleosome remodeling, Isw1 lacking the SANT domain is able to repress transcription initiation at the MET16 promoter. Thus chromatin remodeling and transcriptional repression are distinct activities of Isw1.