Shugoshin family proteins are involved in various aspects of chromatin regulations, such as chromosome segregation, chromatin structure, and gene expression. In growing yeast and mammalian cells, C-terminal phosphorylation of histone H2A by Bub1 kinase is essential for the localization of Shugoshin proteins to chromatin. Here, we show that in stationary-phase cells, Bub1-mediated H2A phosphorylation is not necessary for chromatin localization of the Shugoshin paralog Sgo2 in Schizosaccharomyces pombe, or for Sgo2-dependent suppression of gene expression in subtelomeric regions. The conserved C-terminal basic domain of Sgo2, which directly binds with phosphorylated H2A, is also dispensable for the localization of Sgo2 to chromatin at stationary phase. Instead, we found that the conserved N-terminal coiled-coil domain and the uncharacterized medial region of Sgo2 are required for Bub1-independent localization of Sgo2. Moreover, Set2-mediated H3K36 methylation was important for the regulation. Intriguingly, the chromatin localization of Sgo2 in the absence of Bub1 was also observed when cells were grown in low-glucose medium. These findings suggest a novel mechanism between nutrient availability and regulation of chromatin by Shugoshin proteins.