The development of multicellular life commences with a single fertilized egg, which undergoes continuous cellular division and differentiation, giving rise to a wide array of tissue and organ types, ultimately culminating in the formation of a fully developed individual. Despite sharing the same genome sequence, intricate transcriptional networks orchestrate cellular diversity and manifest distinct phenotypes during the course of multicellular organism development. The interplay between signal transduction pathways, transcription factors, and epigenetic regulation governs gene expression patterns in cells, which typically necessitate stable maintenance once the organism reaches full maturity. Epigenetics encompasses functional alterations in gene expression without changes to the DNA sequence itself, ultimately leading to heritable phenotypic outcomes. Factors contains covalent modifications of DNA and histones, chromatin conformation and higher-order structure dynamics, non-coding RNA molecules among others. Epigenetic regulation assumes a pivotal role in organismal development as well as disease pathogenesis. Changes in chromatin packaging and gene transcriptional activity impact pluripotency establishment and maintenance, cell fate determination and lineage differentiation processes along with cellular function modulation and homeostasis regulation mechanisms. Although numerous types of epigenetic modifications alongside their associated enzymes have been reported thus far; further investigations are warranted to elucidate their dynamic nature as well as functional roles within physiological states or pathological conditions. Utilizing state-of-the-art molecular biology techniques, imaging methods, algorithmic tools, artificial intelligence, and embryonic models, we explore the intricate relationship between epigenetics and its role in both development and disease.