An organism is required to identify biologically relevant protein interactions. We propose Drosophila and its indirect flight muscles as a suitable experimental system for genetic screenings for muscle protein interactions. The first attempt focused on troponin I (TnI) in view of the key role in thin filament regulation that this protein performs. Suppressors of a defined Tn I allele have been isolated as mutations in the heavy chain of myosin (MhC). This unsuspected functional interaction between TnI and MhC serves to illustrate one of the benefits of the approach. Four of the suppressors identified to date reside in the MhC head, around the actin-binding site and near the lips of the pocket where ATP is hydrolyzed. Two other suppressors correspond to a second site mutation in TnI and a mutation in the conserved region of Tropomyosin II (TmII), respectively. All the identified suppressors are mutations in constituents of the sarcomere, and most of them are structurally similar to human mutations causing familial hypertrophic cardiomyopathy (FHC). At least seven sarcomere proteins can lead to FHC and, consequently, the disease is heterogeneous and difficult to diagnose. In addition, putative natural suppressors may help obscure the origin of FHC. The genetic procedure, used here for muscle proteins, could help diagnose FHC and other myopathies, and extend to proteins of clinical interest in other tissues, including the nervous and circulatory systems.