To this end, validated chemoinformatic approaches provide a systematic and rigorous manner to characterize the contents, chemical diversity, and, in general, coverage of the compound libraries in chemical space. The goal of this study is to rigorously characterize the chemical content, diversity, and drug-like properties of eleven epigenetic-focused libraries containing more than 50,000 compounds in total. All data sets are available in the public domain. To the best of our knowledge, this is the first systematic chemoinformatic analysis of epigenetic-focused compound libraries. As part of the analysis, we implemented a recently introduced and validated methodology to compute and identify core structures and analog series based on retrosynthetic rules. The analog series were the basis to generate Constellation Plots as a rich representation of the chemical space that combines substructure and fingerprint representations. For each epigenetic-focused data set, we identified the most frequent core structures. We also generate novel representations of the chemical space using the concept of Extended Chemical Space Networks (eCSNs) and rapidly identify the most representative individual molecules (i.e., medoids) in a large data set: these chemical structures can be used as a "chemical structural marker" or "chemical diagnostic molecules." Herein, we discuss the most representative chemical structures of the epigenetic libraries that can be used as a criterion for comparing the chemical libraries and prioritization for follow-up studies, including computational and experimental screening.