Aristobulus was the younger son of Alexander Jannaeus, King and High Priest, and Alexandra Salome. After the death of Alexander in 79 BC, his widow succeeded to the rule of Judea and installed her elder son Hyrcanus as High Priest. When Salome died in 67 BC, Hyrcanus succeeded to the kingship as well.

Rebellion

Hyrcanus shared his mothers religious views, sympathetic to the Pharisees. In contrast to this, Alexander Jannaeus had supported the Saducees.

Aristobulus agreed with his father's Saducean stance and rebelled against his elder brother. Hyrcanus advanced against him at the head of his mercenaries and his followers. The brothers met in battle near Jericho and many of Hyrcanus' soldiers went over to Aristobulus, and thereby gave the latter the victory.

Hyrcanus took refuge in the citadel of Jerusalem; but the capture of the Temple by Aristobulus compelled Hyrcanus to surrender. A peace was then concluded, according to the terms of which Hyrcanus was to renounce the throne and the office of high priest, but was to enjoy the revenues of the latter office.

This agreement however did not last, as Hyrcanus feared that Aristobulus was planning his death and took refuge with Aretas III, King of the Nabataeans. The Nabataeans advanced toward Jerusalem with an army of 50,000 and besieged the city for several months.

Roman intervention

During this civil war, the Roman general Gnaeus Pompeius Magnus defeated the Kingdoms of Pontus and the Seleucids. He sent his deputy Marcus Aemilius Scaurus to take possession of Seleucid Syria.

As the Hasmoneans were allies of the Romans, both brothers appealed to Scaurus, each endeavoring by gifts and promises to win him over to his side. Scaurus, moved by a gift of 400 talents, decided in favor of Aristobulus and ordered Aretas to withdraw his army. During his retreat, the Nabateans suffered a crushing defeat at the hands of Aristobulus.

When Pompey arrived in Syria in 63 BCE, both brothers and a third party that desired the removal of the entire dynasty, sent their delegates to Pompey, who however delayed the decision. He favoured Hyrcanus over Aristobulos, deeming the elder, weaker brother a more reliable ally of the Roman Empire.

Aristobulos, suspicious of Pompey, entrenched himself in the fortress of Alexandrium, but when the Romans summoned their army, he surrendered and undertook to deliver Jerusalem over to them. However, since many of his followers however were unwilling to open the gates, the Romans besieged and captured the city by force, badly damaging city and temple. Hyrcanus was restored as High Priest, but deprived of political authority.

Aristobulus was on his way to Judaea with his son Alexander, in 49 BC when he was assassinated by poison.

In 40 BCE, Aristobulus' son Antigonus allied himself with the Parthians and was proclaimed King and High Priest. Hyrcanus was seized and mutilated at his ears (according to Josephus, Antigonus bit his uncle's ears off) to make him permanently ineligible for the priesthood. 

Then Hyrcanus was then taken to Babylonia, where for four years he lived amid the Babylonian Jews, who paid him every mark of respect.

In 36 BCE, Herod, who had vanquished Antigonus with Roman help and feared that Hyrcanus might induce the Parthians to help him regain the throne, invited the former High Priest to return to Jerusalem. Hyrcanus accepted and Herod received him with every mark of respect, assigning to him the first place at his table and the presidency of the state council.

However, in 30 BCE Herod charged Hyrcanus with plotting with the Nabateans and put him to death.