It lies immediately behind the last gill-slit. In Balanoglossus the differentiation of dorsal and ventral parts of pharynx continues for a short distance into the oesophagus. In the oesophagus, the dorsal part is called post branchial canal which is lined by a thick glandular and folded epithelium. The posterior part reduces in diameter and possesses deeply furrowed epithelium. In some species (Harrimania, Saccoglassus etc.) the oesophagus communicates with the exterior by means of 1 -15 pairs of minute oesophageal openings out by dorsally situated minute pores. The oesophageal canals are present in the posterior part of oesophagus and are supposed to be remnants of gill-slits.
It is the longest pan of the alimentary canal. It is distinguishable into anterior hepatic region and posterior post-hepatic region. The dorsal wall of the hepatic region is thrown into numerous prominent outgrowths called hepatic caeca. The hepatic region is richly supplied with blood.
Histologically, it shows the presence of many epithelial gland cells containing green or brown inclusions. This region cannot be called as hepatic because it docs not show any homology with the liver of vertebrates.
The post-hepatic part runs straight upto anus. It has wide lumen. It is lined with ciliated epithelium. Its walls are provided with numerous sinuses filled with blood. Dorso- laterally the intestine shows the presence of two well-developed ciliated grooves, sunken in the depressions symmetrically on both the sides. The hinder-most part of the intestine provided with a stiff pygochord, which is connected with ventral body wall. In Harrimunia, the last part of intestine is distinguished as a short rectum. The anus is the last part of alimentary canal provided with anal sphincter.