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809年拉西德死于征途，阿明即位于巴格达，不久，阿明废马蒙，改立长子穆萨为继承人。同年马蒙向他发动攻击，内战于焉展开，阿拉伯人拥护阿明，波斯人拥护马蒙。813年9月26日马蒙攻陷巴格达，阿明被杀，内战结束。马蒙即位于木鹿，取得教主之位。而曼斯尔建立的园形宫城也在内战期间被破坏殆尽。
Caliph
Muhammad ibn Jarir al-Tabari records that Harun al-Rashid several times impressed on his sons they should respect each other and honour the succession as Harun arranged it. In A.H. 186, Harun had al-Amin and al-Ma'mun sign pledges during a pilgrimage to Mecca that both would honour his will. Al-Amin, would receive the Caliphate and al-Ma'mun would become governor of Khurasan in eastern Iran and would furthermore be granted almost complete autonomy. On al-Amin's death, according to Harun's decision, al-Ma'mun would become Caliph.
Hostility towards al-Mamun
Al-Ma'mun had distrusted al-Amin before their father's death and convinced Harun to take him with him on Harun's last journey east. Although Harun had instructed the Baghdad commanders of this expedition to remain with al-Ma'mun, after Harun's death they returned to Baghdad. Al-Amin sought to turn al-Ma'mun's financial agent in Rayy against al-Ma'mun and he ordered al-Ma'mun to acknowledge al-Amin's son Musa as heir and return to Baghdad. Al-Ma'mun replaced his agent in Rayy and refused the orders. His mother was Persian and he had strong support in Iran.
The brothers had different mothers. Al-Amin was prompted to move against al-Ma'mun by meddlesome ministers, especially al Fadl ibn ar Rabi. Al-Amin had Harun's succession documents brought from Mecca to Baghdad, where he destroyed them. Al-Amin sent agents east to stir opposition to al-Ma'mun. However, a careful watch at the frontier denied these the opportunity. Al-Amin denied al-Ma'mun's request for his family and money and kept them in Baghdad.
Battle of Rayy
In March 811 Al-Amin dispatched an army under Ali ibn Isa ibn Mahan against Al-Ma'mun. Ali advanced on Rayy. Ma'mun's capable general Tahir bin Husain met and defeated Ali who was killed.
Internal rebellions
Al-Amin faced unrest in Syria. He sent Abd al-Malik ibn Salih to restore order there. There was fierce fighting and Abd al-Malik died. Al-Amin sent Ahmad ibn Mazyad and Abdallah ibn Humayd east, each with an army (al-Tabari v. 31 p. 100 says each had 20,000 men). However, Tahir's agents sowed discord and these two armies fought against each other.
Al-Amin faced an uprising in Baghdad led by Ali ibn Isa's son Husayn. This was quelled and Husayn was killed. Tahir took Ahwaz and gained control of Bahrayn and parts of Arabia. Basra and Kufa swore allegiance to al-Ma'mun. Tahir advanced on Baghdad and defeated a force sent against him. In Mecca, Dawud ibn Isa reminded worshippers that al-Amin had destroyed Harun ar Rashid's succession pledges and led them in swearing allegiance to al-Mamun. Dawud then went to Marv and presented himself to al-Ma'mun. Al-Ma'mun confirmed Dawud in his governorship of Mecca and Medina.
Siege of Baghdad (812–813)
Tahir advanced and set up camp near the Anbar Gate. Baghdad was besieged. The effects of this siege were made more intense by the rampaging prisoners who broke out of jail. There were several vicious battles, such as at al-Amin's palace of Qasr Halih, at Darb al- Hijarah and al-Shammasiyyah Gate. In that last one Tahir led reinforcements to regain positions lost by another officer. Overall the situation was worsening for al-Amin and he became depressed.
When Tahir pushed into the city, al-Amin sought to negotiate safe passage out. Tahir reluctantly agreed on the condition al-Amin turn over his sceptre, seal and other signs of being caliph. Al-Amin tried to leave on a boat, apparently with these indications he was caliph. He rejected warnings he should wait. Tahir noticed the boat. Al-Amin was thrown into the water, swam to shore, was captured and brought to a room where he was executed. His head was placed on the Anbar Gate. Al-Tabari (v. 31 pp. 197-202) quotes Tahir's letter to al-Ma'mun informing that caliph of al-Amin's capture and execution and the state of peace resulting in Baghdad.
Legacy
The fact that Al-Amin was known to be fond of eunuchs was seen by many at the time as a deficit in his character. Al-Tabari notes this fondness for eunuchs. He also records accounts of al-Amin's intense irritation when singers sang songs that were not very auspicious. Al-Amin is described by this historian as being extravagant.
Al-Amin had appealed to his mother, Zubaida, to arbitrate the succession and champion his cause as Aisha had done two centuries before. Zubaida refused to do so.