Dynamic changes in chromatin structure are crucial for diverse biological processes. Given the complexity of the epigenetic landscape, understanding the specificity of chromatin modification has been a major interest in the epigenetics field. Recent progress in biochemical and structural analyses in the field of chromatin biology has revealed that recognition of allosteric effectors and the subsequent conformational change(s) are central to the regulation of catalytic activities and functions of chromatin modifying enzymes. Here, we review several examples of distinctive nucleosome features, including DNA methylation, histone modifications, and variable-length linker DNA, that allosterically regulate the enzymatic activities of chromatin modifiers to confer functional specificity in a given chromatin context. We further highlight the biological significance of these allosteric mechanisms and discuss their potential as emerging targets for selective modulation of chromatin architecture.