Microtia, a congenital anomaly of the external ear, serves as a model to explore the intricate synergy between genetics and epigenetics in shaping phenotypic outcomes. Genetics, residing in DNA, provides the blueprint for development, while epigenetic modifications modulate gene expression without altering the DNA sequence. This comprehensive review delves into their combined influence on microtia's etiology, unravelling the significance of DNA methylation, histone modifications, and microRNAs in ear formation and their susceptibility to environmental cues. Genetic investigations encompass pedigree analysis and whole-exome sequencing, spotlighting pivotal genes like HOXA4 and CHST15. Syndromic associations underscore the multifaceted genetic underpinning of microtia. This dynamic interplay between genetics and epigenetics enriches our understanding of developmental anomalies, offering insights for tailored interventions and clinical strategies to manage this condition in a personalized manner. The continuous exploration of these interactions opens avenues for deciphering intricate developmental processes and expanding our comprehension of related anomalies.