Abstract Background Deciphering the genetic architecture of cardiac disorders is of fundamental importance but their underlying complexity is a major hurdle. Drosophila has gained importance as a useful model to study heart development and function and allows the analysis of organismal traits in a physiologically relevant and accessible system. Our aim was to (i) identify in flies the loci associated to natural variations of cardiac performances among a natural population, (ii) decipher how these variants interact with each other and with the environment to impact cardiac traits, (iii) gain insights about the molecular and cellular processes affected, (iv) determine whether the genetic architecture of cardiac disorders is conserved with humans. Methods and Results We investigated the genetic architecture of natural variations of cardiac performance in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP). Genome Wide Associations (GWA) for single markers and epistatic interactions identified genetic networks associated with natural variations of cardiac traits that were extensively validated in vivo. Non-coding variants were used to map potential regulatory non-coding regions which in turn were employed to predict Transcription Factors (TFs) binding sites. Cognate TFs, many of which themselves bear polymorphisms associated with variations of cardiac performance, were validated by heart specific knockdown. We also analyzed natural variations of cardiac traits variance that revealed unique features of their micro-environmental plasticity. More importantly, correlations between genes associated with cardiac phenotypes both in flies and in humans support the conserved genetic architecture of cardiac functioning from arthropods to mammals. The characteristics of natural variations in cardiac function established in Drosophila may thus guide the analysis of cardiac disorders in humans. Using human iPSC-derived cardiomyocytes, we indeed characterized a conserved function for PAX9 and EGR2 in the regulation of the cardiac rhythm Conclusion In-depth analysis of the genetic architecture of natural variations of cardiac performance in flies combined with functional validations in vivo and in human iPSC-CM represents a major achievement in understanding the mechanisms underlying the genetic architecture of these complex traits and a valuable resource for the identification of genes and mechanisms involved in cardiac disorders in humans.