Intelectin is a soluble lectin known as a pattern-recognition receptor for the innate immune system or as an intestinal lactoferrin receptor. Intelectin genes have been identified in a wide range of chordates and the shared expression pattern in their absorptive intestinal regions has been widely recognized. The chordate intelectins have a shared domain structure with a fibrinogen-related domain and an intelectin domain and an additional sequence has been reported only in ascidian Ciona intestinalis intelectins. However, little is known about the molecular features of the ascidian intelectins, including the distribution of the additional sequence in ascidians. Therefore, we focus on the ascidian species that are available for genome DNA sequence searches and survey intelectin genes with special reference to the additional sequence. We also assess the distribution of Ciona intelectin gene transcripts in transparent juveniles and adult specimens by means of in situ hybridization and reveal hemocyte-dominant expressions as well as stomach-exclusive expression. Comparative gene expression analysis with secretory digestive enzymes and absorption-related proteins in Ciona revealed that intelectin and secretory digestive enzymes were expressed in the same region of the stomach epithelium. Since the domain structure of intelectins and the hemocyte-dominant gene expression of intelectins seem relevant to ficolin, intelectin genes may have evolved from a ficolin-like ancestral gene with hemocytic expression in early chordate evolution.