Apsyrtus was born in Colchis, the wealthy kingdom on the eastern shore of the Black Sea where the golden ram had once flown and where its fleece now hung in a grove sacred to Ares, the god of war. His father was Aeetes, the son of Helios and the Oceanid Perseis, a king whose palace was famous for its brazen walls and its gardens of magical herbs. His mother was Asterodeia, a Caucasian nymph, though some say she was Eidyia, the youngest daughter of the Titans Oceanus and Tethys, or even the goddess Hecate. He had an older sister named Medea, a priestess of Hecate who knew the secrets of drugs and poisons, and another sister named Chalciope, who had married Phrixus, the man who had arrived in Colchis on the back of the flying ram. Apsyrtus grew up in his own palace, a building of gold and bronze that stood beside the loftiest structure in the city, a mark of his father's favour and his position as heir.

Before the Argonauts ever reached Colchis, Apsyrtus had already proved himself in war. When Perses, the brother of Aeetes, came with a Scythian army to seize the throne, Apsyrtus rode to the front line in armour of gold. He drove the chariot of his grandfather Helios, and his golden shield was so bright that common men could not gaze upon it without pain. He charged the enemy, trampled them beneath his horses, and drove them from the field. Aeetes kept his throne, and the Argonauts, who had arrived during the siege, were promised the Golden Fleece in return for their aid. But when the war was won, Aeetes went back on his word. He set Jason impossible tasks - yoking fire-breathing oxen, sowing dragon's teeth that sprang up as warriors - and when Jason completed them all through Medea's magic, the king plotted to kill the hero and keep the fleece.

Medea, who had fallen in love with Jason, betrayed her father. She gave Jason a drug to protect him from the oxen's flames, told him to throw a stone among the earth-born warriors to make them turn on one another, and led him by night to the grove where the fleece hung, lulling the never-sleeping dragon to sleep with her enchantments. Then she fled with him. Some say she took Apsyrtus with her as a hostage, a child in her arms. Others say she left him behind and he was sent by his father to hunt her down. In the oldest version of the tale, preserved in fragments, Medea carried her young brother aboard the Argo, and when Aeetes' fleet drew close behind them, she took a blade, cut Apsyrtus into pieces, and scattered his limbs across the waves. Aeetes, seeing the body parts of his only son floating in the water, ordered his ships to stop and gather them for burial. The delay gave the Argo the time it needed to escape. The place where this happened was called Tomi, from the Greek word for "cut," and the islands nearby were named the Absyrtides in his memory.

In the version told by Apollonius of Rhodes in his Argonautica, Apsyrtus was no child but a man and a commander. Aeetes placed him at the head of the Colchian navy and sent him to recover both the fleece and the traitorous daughter. Apsyrtus proved a cunning strategist. He divided his fleet, sending part of it up the Danube to get ahead of the Argo and block its escape. He caught up with Jason and Medea at the Brygean Islands, a cluster of rocks sacred to Artemis, the virgin huntress goddess. Realising they were cornered, Medea devised a trap. She sent a message to her brother saying that she wished to meet him alone, that she would return the fleece, and that together they could sail back to Colchis and their father. Apsyrtus, honourable and trusting, landed on the island by himself. He walked to the temple of Artemis, and there Jason lay in wait. The hero struck him down with his sword, and then, to prevent the dead man's ghost from seeking vengeance, he and Medea mutilated the body. The Colchians who came looking for their commander the next morning found a horror that made them weep. Some gathered the remains and sailed home to give Apsyrtus a fitting burial. Others, fearing Aeetes' wrath, scattered across the coasts and founded new settlements.

The murder of Apsyrtus was not a crime that the gods would overlook. When Jason and Medea reached the island of Aeaea, they sought out Circe, Medea's aunt and a powerful sorceress. Circe was horrified by what they had done. She performed the rites of purification, cleansing them of the blood-guilt that clung to their hands, but her face showed no forgiveness. The Erinyes, the avenging spirits of kin-murder, had already marked them. The death of Apsyrtus would haunt Medea for the rest of her life, a sin that compounded with every later crime - the murder of Pelias, the killing of her own children, the burning of the Corinthian bride. Some ancient critics saw in Apsyrtus' death the moment when Medea crossed a line from which she could never return, the first act in a career of violence that would make her the most notorious woman in Greek myth.