MOSCOW — Russia’s unyielding support for Damascus throughout the 16 months of Syria’s escalating crisis has earned Moscow strong condemnation from Washington and other Western governments, but the reasons for Russia’s implacable position have never been fully explained by Moscow or its critics.

Washington’s latest tension with Russia over Syria came last week in a face-to-face meeting between President Barack Obama and President Vladimir Putin. The week before U.S. Secretary of State Hillary Clinton called Russia’s assertion that it sold only defensive weapons to Damascus “patently untrue.” That was after Clinton had accused Russia of shipping attack helicopters to Syria to crush the rebellion, a charge denied by Moscow. The New York Times then reported that Russia was only returning repaired helicopters sold to Syria decades ago.

In February, Susan Rice, the top U.S. diplomat at the UN, used undiplomatically strong language to say the U.S. was “disgusted” by Russia’s veto of a Security Council resolution that would have condemned the Syrian crackdown. The tough talk appears designed to embarrass Russia, especially after the recent upsurge in fighting and a string of grisly massacres blamed on Moscow’s client.

But until now Russia’s motives for defending Damascus have remained largely a subject of speculation, with the U.S. media seemingly disinterested in exploring it.

Russian officials say their position is based on an adamant opposition to regime change, particularly if it is led by Western military intervention, as in Libya. Moscow’s support for the Syrian regime has not changed though it has recently inched away from President Bashar Al-Assad leading it.

Analysts routinely cite three additional reasons for Moscow’s Syria policy: Russia’s millions of dollars a year in legal arms sales to Syria, Russian naval access to a port at Tartus on Syria’s Mediterranean coast and a desire to maintain its last ally in the Middle East.

But a clearer image of Russia’s stance comes into focus when put in the context of Moscow’s 30-year struggle against encroachment into its sphere of influence by militant Islam. The support at times given these groups by the U.S. and Gulf Arab nations has opened a three-decade rift with Russia that began in Afghanistan and has run across the Northern Caucasus to the Balkans and now into Syria.

Russia is opposed to regime change in Syria not only on principle, but because the likely new regime would be headed by an Islamist government inimical to Russian interests, analysts and diplomats say.

“You can talk about arms sales, and the port, but the real thing that Russia is worried about is an Islamic government coming to power in Syria,” said a senior Western diplomat, who would only speak on condition of anonymity because of the current tension in Western-Russian relations.

“Russia is obviously concerned about Islamic regimes and perhaps most important of all it is terrified of chaos,”” said Mark Galeotti, who chairs the Centre for Global Affairs at New York University. He said chaos and anarchy in the Middle East fuel the rise of Islamic extremism.

“Russia feels that the West doesn’t know how to handle regime change and that the outcome is almost invariably the kind of the chaos from which Islamic extremist movements arise,” Galeotti said.

The dominant member of Syria’s opposition is the Muslim Brotherhood, suppressed for 40 years by President al-Assad and his father Hafiz al-Assad before him. The discord in the Syrian opposition arises largely from differences between the Brotherhood and secular liberal groups, the Western diplomat said. The emergence of al-Qaeda affiliated groups, responsible for several bombings, has added a menacing dimension.

“There is a general sense in Moscow that if Syria fell to extremists’ hands the whole Middle East could explode, which is also a security concern for the Russians,” Galeotti said.

Russia’s struggle against Islamism has its roots in the 1979 to 1989 Afghan conflict, in which the Soviet Union ultimately failed with helicopter gunships and ground troops to defeat militant mujahedeen, armed with weapons, cash and intelligence from Washington, Riyadh and Islamabad. Shoulder-fired American Stinger rockets came to symbolize the conflict as they blasted Soviet helicopters out of the sky.

Russian troops withdrew in defeat in February 1989. The Soviet Union collapsed in December 1991 with analysts pointing to the Afghan debacle as a primary cause. Out of the war emerged Osama bin Laden’s al-Qaeda network, which later came to wreak havoc on its former sponsors.

Washington policymakers typically employ a short-term foreign policy that later comes back to haunt them, analysts said. From the Islamists’ point of view it is hard to turn down American arms and financing when policies are aligned, and then implement its agenda once it is helped to seize power.

“Afghanistan [under the pro-Moscow regime] was a secular government, women were not forced to cover, they were given suffrage, yes it was a dictatorship, but the U.S. helped … overthrow [it] and replaced it with a religious, dogmatic theocracy that destroyed Afghanistan,” said Ali al-Ahmed, director of the Institute for Gulf Affairs in Washington.

“They are doing the same thing in Syria,” he said, predicting a failed state with uncontrolled, armed groups threatening the region. “You will see Afghanistan emerging in Syria next door to Israel and it will be a huge, huge problem for the United States,” with Lebanon devolving into the equivalent of Pakistan, he said.

The unfortunate choice in Syria is between a Russian-backed secular dictatorship, which allows freedom of religion and protects Christians, Alawis and Sunni businessmen, or a U.S.- and Gulf-supported religious dictatorship with even fewer freedoms, al-Ahmed said. “They are repeating their history and Russia was both times on the other side,”” al-Ahmed said.

The collapse of the Soviet Union after the Afghanistan defeat opened former Soviet republics in the Caucuses to an Islamic insurgency helped by the U.S. and the Gulf that still troubles Moscow.

“Chechnya is a classic example of what goes wrong when things go out of hand,” said Galeotti. “The West thought they would be politically supporting nationalists, reasonable figures and they wind up creating a situation in which Islamic fundamentalists, terrorists and suicide bombers found a haven.”

In the Balkans, Russia defended its traditional Slavic and Orthodox Christian Serb allies — against separatist Croatians and Bosnian Muslims, whom the International Criminal Court accused of hosting an al-Qaeda unit known as the “El Mujahedeen.”

Dmitri Simes, a former adviser to President Richard Nixon who heads the Center for the National Interest in Washington, says he still hears “a lot of anger”” from Russian officials over what “the Clinton administration did in the Balkans.”

He see a parallel in Syria where Russian officials are especially concerned about the fate of Christians if Islamists take over. “They are concerned that Muslim fundamentalists, not just the Musim Brotherhood, but people more extreme might come to power and it would be destabilizing for the region,” Simes said. “But as Syria is not a Russian neighbor a possible massacre of Christians would be seen as a greater problem.”

Russia might be willing to do a deal to try to ease out al-Assad, which it sees as a liability, if the U.S. would offer something in return, such as an agreement on missile defense, he said. “If that was made clear to Russian officials perhaps Putin would be prepared to deal,” Simes said. “But he is simply told that his position is morally inferior.”

In the absence of a deal Moscow strongly fears Western military intervention to overthrow yet another Russian ally, Simes said, leading to chaos.

Moscow is willing to deal because it had “no great sympathy for Assad even before he was in full massacre mode” and is backing away, realizing that “a regime like Assad’s is ot in the long run sustainable,” said Galeotti.

“If it were clear that regime change were not on the cards, I think Russia would be a lot more willing as allies and interlocutors,” he said. “They are digging their heels in because they feel that the only policy the West is willing to push is regime change.”

Moscow would ideally prefer “a controlled, steady reformist who could in some ways manage the process and not allow Islamic fundamentalists to dominate the narrative,” Galeotti said.

Russia thinks Washington’s motive to remove al-Assad is to weaken Iran at almost any cost, Simes said.

The U.S. does not publicly discuss what it believes Russia’s motives are for backing Syria, leaving the impression that moral deficiency makes it complicit with Damascus.

The closest the U.S. has come to acknowledging Russia’s fear of an Islamist regime in Syria and America’s own apparent tolerance for it came from a cryptic remark by Clinton in the UN Security Council chamber last March with Russian Foreign Minister Sergei Lavrov sitting across from her.

“I know there are those who question whether Islamist politics can really be compatible with … democratic and universal principles and rights,” Clinton said. “Our policy is to focus less on what parties call themselves than on what they choose to do.” Lavrov did not respond.