This phylogenomic study shows that core muscle proteins were already present in unicellular organisms before the origin of multicellular animals, and supports a convergent evolutionary model for striated muscles in which new proteins are added to ancient contractile apparatus during independent evolution of bilaterians and some non-bilaterians, resulting in very similar ultrastructures. The ultrastructural similarity between striated skeletal muscles in higher bilaterian animals, such as humans and insects, and non-bilaterian animals, such as jellyfish, suggests a common evolutionary origin of this important contractile cell type. However, the precise evolution of striated muscles has not been confirmed. In this phylogenomic study, Ulrich Technau and colleagues show that core muscle proteins are present in unicellular organisms, such as sponges, that do not have true muscles. Their analysis supports a convergent-evolution model for striated muscles. According to this model, novel proteins were added to the ancient contractile apparatus during the independent evolution of the cnidarians and bilaterians, resulting in strikingly similar ultrastructures. Striated muscles are present in bilaterian animals (for example, vertebrates, insects and annelids) and some non-bilaterian eumetazoans (that is, cnidarians and ctenophores). The considerable ultrastructural similarity of striated muscles between these animal groups is thought to reflect a common evolutionary origin1,2. Here we show that a muscle protein core set, including a type II myosin heavy chain (MyHC) motor protein characteristic of striated muscles in vertebrates, was already present in unicellular organisms before the origin of multicellular animals. Furthermore, ‘striated muscle’ and ‘non-muscle’ myhc orthologues are expressed differentially in two sponges, compatible with a functional diversification before the origin of true muscles and the subsequent use of striated muscle MyHC in fast-contracting smooth and striated muscle. Cnidarians and ctenophores possess striated muscle myhc orthologues but lack crucial components of bilaterian striated muscles, such as genes that code for titin and the troponin complex, suggesting the convergent evolution of striated muscles. Consistently, jellyfish orthologues of a shared set of bilaterian Z-disc proteins are not associated with striated muscles, but are instead expressed elsewhere or ubiquitously. The independent evolution of eumetazoan striated muscles through the addition of new proteins to a pre-existing, ancestral contractile apparatus may serve as a model for the evolution of complex animal cell types.