The analysis of both naturally occurring and experimentally induced mutants has greatly advanced our understanding of muscle development. Molecular biological techniques have led to the isolation of genes associated with inherited human diseases that affect muscle tissues. Analysis of the encoded proteins in conjunction with the mutant phenotypes can provide powerful insights into the function of the protein in normal muscle development. Systematic searches for muscle mutations have been made in experimental systems, most notably the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. In addition, known muscle protein genes from other organisms have been used to isolate homologs from genetically manipulatable organisms, allowing mutant analysis and the study of protein function in vivo. Mutations in transcription factor genes that affect mesoderm development have been isolated and genetic lesions affecting myofibril assembly have been identified. Genetic experiments inducing mutations and rescuing them by transgenic methods have uncovered functions of myofibrillar protein isoforms. Some isoforms perform muscle-specific functions, whereas others appear to be replaceable by alternative isoforms. Mutant analysis has also uncovered a relationship between proteins at the cell membrane and the assembly and alignment of the myofibrillar apparatus. We discuss examples of each of these genetic approaches as well as the developmental and evolutionary implications of the results.