The N-terminal actin-binding domain of α-actinin is connected to the C-terminal EF-hands by a rod domain. Because of its ability to form dimers, α-actinin can cross-link actin filaments in muscle cells as well as in nonmuscle cells. In the prototypic α-actinins, the rod domain contains four triple helical bundles, or so-called spectrin repeats. We have found some atypical α-actinins in early diverging organisms, such as protozoa and yeast, where the rod domain contains one and two spectrin repeats, respectively. This implies that the four repeats present in modern α-actinins arose after two consecutive intragenic duplications from an α-actinin with a single repeat. Further, the evolutionary gene tree of α-actinins shows that the appearance of four distinct α-actinin isoforms may have occurred after the vertebrate-invertebrate split. The topology of the tree lends support to the hypothesis that two rounds (2R) of genome duplication occurred early in the vertebrate radiation. The phylogeny also considers these atypical isoforms as the most basal to α-actinins of vertebrates and other eukaryotes. The analysis also positioned α-actinin of the fungi Encephalitozoo cuniculi close to the protozoa, supporting the suggestion that microsporidia are early eukaryotes. Because α-actinin is considered the basal member of the spectrin family, our studies will improve the understanding of the origin and evolution of this superfamily.