Left-right asymmetric expression of Pitx as well as of Nodal has been observed in some ascidian species, but a mechanism that regulates the asymmetric expression of Pitx remains largely unclear. We addressed the transcription regulatory mechanism of the left-right asymmetric expression of Pitx gene in the ascidian, Ciona intestinalis. We first identified an intronic enhancer that drives Ci-Pitx left-sided expression in the epidermis and found that a single FoxH1 binding site present in this enhancer is essential for its activity. Also, we have shown that the enhancer requires Nodal signaling to drive the Ci-Pitx expression in the left epidermis. In C. intestinalis, left-sided expression of the Nodal gene has not been reported so far. We have confirmed that Ci-Nodal is expressed in the left epidermis of embryos at the tailbud stage only when they are allowed to develop within the chorion. Then, to test the importance of the FoxH1 binding site, we carried out knock down experiments using morpholino antisense oligonucleotides against Ci-FoxHa, the only FoxH gene that is expressed in the same stage as the left-sided expression of Ci-Pitx is observed. Knocking down of the function of Ci-FoxHa led to the down regulation of the expression of Ci-Pitx in the left epidermis. The present results suggest that the regulatory mechanism controlling the left-right asymmetric expression of the Pitx genes is well conserved between C. intestinalis and vertebrates.