Independence

Soldiers during the civil war, 1992.

Tajik men and women rally on Ozodi square in Dushanbe shortly after independence, 1992.

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 theCommonwealth 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                                             .Russian border troops were stationed along the Tajik–Afghan border until summer 2005. Since the September 11, 2001 attacks, French troops have been stationed at the Dushanbe Airport in support of air operations of NATO's International Security Assistance Force in Afghanistan. United States Army and Marine Corps personnel periodically visit Tajikistan to conduct joint training missions of up to several weeks duration. The Government of India rebuilt the Ayni Air Base, a military airport located 15 km southwest of Dushanbe, at a cost of $70 million, completing the repairs in September 2010. It is now the main base of the Tajikistan air force. There have been talks with Russia concerning use of the Ayni facility, and Russia continues to maintain a large base on the outskirts of Dushanbe.

In 2010, there were concerns among Tajik officials that Islamic militarism in the east of the country was on the rise following the escape of 25 militants from a Tajik prison in August, an ambush that killed 28 Tajik soldiers in the Rasht Valley in September, and another ambush in the valley in October that killed 30 soldiers,followed by fighting outside Gharm that left 3 militants dead. To date the country's Interior Ministry asserts that the central government maintains full control over the country's east, and the military operation in the Rasht Valley was concluded in November 2010. However, fighting erupted again in July 2012. In 2015 Russia will send more troops to Tajikistan, as confirmed by a report of STRATFOR (magazine online)

In May 2015, Tajikistan's national security suffered a serious setback when Colonel Gulmurod Khalimov, commander of the special-purpose police unit (OMON) of the Interior Ministry, defected to the Islamic State.