The nation almost immediately fell into civil war that involved various factions fighting one another; these factions were often distinguished by clan loyalties. More than 500,000 residents fled during this time because of persecution, increased poverty and better economic opportunities in the West or in other former Soviet republics. Emomali Rahmon came to power in 1992, defeating former prime minister Abdumalik Abdullajanov in a November presidential election with 58% of the vote. The elections took place shortly after the end of the war, and Tajikistan was in a state of complete devastation. The estimated dead numbered over 100,000. Around 1.2 million people were refugees inside and outside of the country. In 1997, a ceasefire was reached between Rahmon and opposition parties under the guidance of Gerd D. Merrem, Special Representative to the Secretary General, a result widely praised as a successful United Nations peace keeping initiative. The ceasefire guaranteed 30% of ministerial positions would go to the opposition. Elections were held in 1999, though they were criticized by opposition parties and foreign observers as unfair and Rahmon was re-elected with 98% of the vote. Elections in 2006 were again won by Rahmon (with 79% of the vote) and he began his third term in office. Several opposition parties boycotted the 2006 election and the Organization for Security and Cooperation in Europe (OSCE) criticized it, although observers from the Commonwealth of Independent States claimed the elections were legal and transparent. Rahmon's administration came under further criticism from the OSCE in October 2010 for its censorship and repression of the media. The OSCE claimed that the Tajik Government censored Tajik and foreign websites and instituted tax inspections on independent printing houses that led to the cessation of printing activities for a number of independent newspapers.

How were the different factions distinguished from eachother?