In ascidians, maternal factor(s) localized in the myoplasm of the egg are essential for specification and subsequent differentiation of larval muscle cells. The macho-1 gene of Halocynthia roretzi encodes a zinc-finger protein: the gene is only expressed maternally, the resultant maternal mRNA is localized to the myoplasm, and the gene function is essential for muscle cell differentiation. Here we have characterized macho-1 homologues, Ci-macho1 of Ciona intestinalis and Cs-macho1 of Ciona savignyi. Interestingly, we found that the Ciona macho-1 genes are expressed both maternally and zygotically: their maternal transcript is localized to the myoplasm while their zygotic expression is seen after neurulation in cells of the central nervous system. Functional suppression of Cs-macho1 with morpholino antisense oligonucleotide resulted in inhibition of the initiation of zygotic expression of a muscle-specific actin gene. We propose a possible evolutionary scenario in which an ancestral Zic-related gene gave rise to both the macho-1-like muscle determinant gene as well as neuronal Zic genes.