In the wide scenery of heart pathologies the field of cardiomyopathies is one of those showing a great unreliability. After years of generic classifications the American Heart Association (AHA 2006) first, the European Society of Cardiology (ESC 2008) and just recently the MOGE'S Classification (2013), signed a decided step forward to depict more accurately the different forms of cardiomyopathies. During the last decades, technology improvement realized an important growing of knowledge, about clinical and diagnostics instrumental assessment of the cardiomyopathies. At the same time, the large diffusion of genetic and molecular diagnostic procedures, represent the powerful tool to create a more accurate correlation, between clinical evidences and genetic and molecular damage. Although the important advancements realized, we are still far away to understand why to determinate DNA aberration may correspond a wide range of cardiomyopathies, especially for hypertrophic (HCM) and dilated (DCM) forms, characterized by a different quality and quantity of myocardial damage. The poor alignment between genotypes and phenotypes of these cardiomyopathies is the main reason that makes this topic still obscure and scarcely understood. The newest and most advanced high throughput next generation sequencing (NGS) technologies, could represent, at the moment, the powerful tool able to realize a complete and rapid sequencing of the whole genome (WGS), exome (WES) or transcriptome. This goal is certainly a starting point for each patient affected of cardiomyopathy, making possible to individuate all the genetic mutations, genomic variations and epigenetic keys implicated in the myocardial structural damage. The aim of this work is to review and update the state of the art of the knowledge on Hypertrophic CM (HCM) and Dilatative CM (DCM).