In the southernmost end of the sanctuary sacred to Zeus in Dodoni, roughly 30m westwards from the gate of the enclosure, rests the temple of Hercules, part of which lied under the Christian Basilica Β. It was built in the early third century BC, in the years of Pyrrhus, the king of Epirus, who made efforts to correlate his genos (larger family, house) with the mythical hero, particularly after his second marriage to Lanassa, daughter of Agathocles, who was the tyrant of Syracuses, and originated from the family of Hercules.

This is the largest temple after that of Zeus, and the only known temple of Doric order within the sanctuary. It is oriented from northwest to southeast and measures 16.50 x 9.50m. Except of the pronaos (front section) and the cella (in Greek, sek?s), the temple also disposes of four or six Doric columns at the fa?ade (tetrastyle or hexastyle prostylos temple). After being set on fire by the Aetolians in 219 BC, it had been reconstructed and the destroyed architectural members of soft sandstone (triglyphs, capitals, cornice) were set in the wall that separates the pronaos from the cella. To the east of the pronaos survives a large pedestal, 5.70 x 3.20m in dimensions, which made part of the altar of the temple.

The fact that the temple was related to the adoration of Hercules is ascertained by several archaic bronze sheets found on the interior, by cheek pieces from helmets, by a relief representation depicting the dispute between Apollo and Hercules for the possession of the Delphic tripod, and especially by a metope made of limestone in the third century BC, depicting in relief the fight of Hercules against the monster called Lernaia Hydra, and is currently included among the exhibits of the Archaeological Museum of Ioannina. The hero is pressing down with his right knee the body of the beast depicted to his right, while Iolaos, standing to the left of Hercules, is trying to burn a tentacle of Hydra with a torch (his right thigh is visible). A crab near the right thigh of Hercules suggests the marsh of Lerna, which was the theatre for this particular scene.