During embryogenesis of ascidians, endoderm cells initiate certain processes associated with differentiation and produce a tissue-specific enzyme, alkaline phosphatase (ALP). ALP has been used as a histochemical marker of endoderm differentiation. In the present study, the temporal profile of ALP expression during embryogenesis was investigated. In Halocynthia roretzi, endoderm-specific ALP is a membrane bound protein and is distinguishable from maternal cytoplasmic ALP by molecular mass. The activity of endodermal ALP first appeared at the early tail-bud stage. Treatment of developing embryos with inhibitors of translation and transcription was started at various stages. The results suggested that the synthesis of endodermal ALP protein started at the early tail-bud stage, and that the transcription of mRNA was initiated in the gastrula. In other ascidians, Ciona and Styela, it has been suggested that a significant amount of maternal ALP mRNA exists in eggs. The present study revealed that there are significant species differences in ALP expression during ascidian embryogenesis.