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Syria's road from French colony (er, I mean "protectorate" or whatever) to the mess it is today was littered with coups d'état: three in 1949, one each in 1951, 1954, 1961, 1963, and 1966, and finally the 1970 Corrective Movement that brought Hafez al-Assad to power. I'm probably missing a couple somewhere along the way. Through it all, Syria transitioned from parliamentary republic to military dictatorship, to leftist military dictatorship, to union with Egypt, to disunion with Egypt, to Baathist military dictatorship, to Syrian Baathist military dictatorship, and at last to the Assad family's fiefdom.
Especially terms of regional significance, the 1966 coup is probably more important than the others, because it was the 1966 coup that splintered the once pan-Arab Baath Party into its two regional branches, in Syria and Iraq. If you ever wondered (and of course you did), back in the days when Saddam Hussein was still with us, why Syria and Iraq were both governed by "the Baath Party" but never got along with one another, it's because of this coup we're talking about today.
The original Baath Party was the ideological offspring of three Syrian intellectuals: Michel Aflaq (d. 1989), Zaki al-Arsuzi (d. 1968), and Salah al-Din al-Bitar (d. 1980). Without going into the biographies of all three of them, the important thing to understand here is that they never worked together—Aflaq and Bitar were close allies, but Aflaq and Arsuzi seem to have had a mutual loathing for each other even though Arsuzi had an influence on Aflaq's thinking. Arsuzi on the one hand, and Aflaq and Bitar on the other, formed competing "Arab Baath Parties" in the 1940s; Arsuzi created his first, and he seems to have suspected that Aflaq was some sort of Western stooge whose job was to usurp the Baathist (the term means something like "renaissance") movement. It was Aflaq's party (Bitar was sort of Engels to Aflaq's Marx, if you will, so when I talk about Aflaq doing something you can assume that Bitar was working with him) that survived and became what we think of today as "the Baath Party."
Both Arsuzi's and Aflaq's parties were rooted in very similar ideologies: a merger of pan-Arabism, which was traditionally a conservative response to European encroachment, with left-wing revolutionary socialism and a kind of "liberty" that would be "protected" by the unelected Baathist party hierarchy. This mix wasn't all that dissimilar to Nasserism, which is probably why Syrian Baathists were eager to unite with Nasser's Egypt as part of the short-lived (1958-1961) United Arab Republic. That union collapsed not over ideological disputes, but because Gamal Abdel Nasser sidelined those Syrian Baathists (along with everybody else from the Syrian government), the better to dominate the union himself. He actually ordered the Baath Party to dissolve.
The UAR affair caused some fracturing within the Baath Party. On the one hand you had those who began to put Syrian nationalism ahead of pan-Arabism ("pan-Arabism" in the UAR basically meant that Nasser ran everything). They're sometimes called "regionalists" or "Neo-Baathists," though it's a bit anachronistic to use that term at this point, as we'll note below. On the other hand you had those, like Aflaq, who still believed in the idea of Arab unity even while they acknowledged that Nasser's control of the UAR was problematic. Essentially, this was a division between Baathists who acknowledged (even if they didn't like it) Nasser's order to dissolve the party (like Aflaq) and those who kept their local Baath branches active in spite of Nasser. Regionalists also seem to have been influenced by Marxism-Leninism to a far greater degree than Aflaq—though Aflaq was also clearly influenced by Marxist-Leninist thinking to some degree, particularly in his views on revolution and the need for a vanguard party. And there were some Syrian Baathists who continued to support Nasser, though at this point it's probably fair to call them "Nasserists" rather than "Baathists."
After the UAR dissolved, Aflaq reformed the Baath Party and ran its National Command, which oversaw the party's two regional commands (in Syria and Iraq). At this point, Baathist ideology really began to take root among the Syrian military establishment, though it was the regionalist flavor that really caught on rather than Aflaq's Baath Classic formulation. The 1963 coup was led by Baathist elements in the Syrian military, along with Nasserists who were hoping that a new Baathist government might try to rejoin the UAR (Egypt retained the UAR's name, hoping for a reunion, until after Nasser's death). Bitar became prime minister in the post-1963 government, so Aflaq and the pan-Arabists clearly still had influence, but things were heading toward a breaking point. The real power in the state now rested with the military leaders of the 1963 coup, who were mostly regionalists: army chief of staff Salah Jadid, new defense minister Muhammad Umran (who was more sympathetic to Aflaq than the other two), and rising star (and Arsuzi acolyte) Hafez al-Assad.
Aflaq (front and center) and Jadid (right, in the hat) shortly after the 1963 coup (Wikimedia Commons)
As an aside, while all of this stuff was going on in Syria, the Baath Party had been making steady political gains in neighboring Iraq. They had worked with Iraqi general Abd al-Karim Qasim in carrying out the 1958 coup that overthrew the Hashemite monarchy and put Qasim in charge of a new Iraqi republic. Baathists, along with the Iraqi military, overthrew Qasim in February 1963, but then were themselves taken out of the equation by Nasserists in the military later that year. The Iraqi Baath branch was undergoing the same metamorphosis as the Syrian branch, from part of a unified international movement to a separate institution, and eventually to one man's entourage (in Iraq's case, replace Assad with Saddam Hussein). But it wasn't until 1968 that the Iraqi Baathists managed to get back into power, and by then the split between the two branches had already solidified.
Anyway, back to Syria. Aflaq and Bitar began to lose prestige as the Syrian economy struggled (wealthy Syrians who were freaked out about the regionalists' Communist leanings were moving their assets out of the country, even though Bitar's government tried to implement a softer brand of socialism). Jadid and Assad (Jadid being the more powerful of the two at this point) began to plot a military takeover of the whole Baathist organization (and therefore of the government). Umran broke with them and warned the civilian government of their plans, but Jadid was able to force him into exile. Civilian regionalists, who were completely fed up with Aflaq's moderation by this point, wholeheartedly backed Jadid's power play. The party's Syrian Regional Command, with Jadid as its nominal #2 (though in reality he was running the show), appropriated unto itself the power to govern Syria. Aflaq rejected this marginalization of his National Command, and consequently he was removed from his leadership of that organization in April 1965 and replaced by a relative outsider to Syrian politics, Munif al-Razzaz.
Razzaz tried to stifle the growing independence of the Syrian Regional Command, but Jadid's position was simply too strong. In late 1965 Razzaz actually ordered the dissolution of the Regional Command, put Bitar back in office as prime minister, and recalled Umran from exile to serve as defense minister. Jadid then staged a crisis. On February 21, 1966, he had the Syrian officer in charge of military units on the Golan Heights report that some kind of mutiny was underway, which forced Umran and Syrian President Amin al-Hafiz to rush there to prevent a catastrophe that could risk war with Israel. Jadid made his move on February 23, shortly after they returned to Damascus, distracted and exhausted. There was some scattered armed resistance throughout the country, but ultimately Jadid had little trouble taking total control over Syria.
Aflaq and Saddam Hussein, 1988 (Wikimedia Commons)
Aflaq was now on the outside looking in, and his old pal Arsuzi actually enjoyed a brief resurgence, becoming the new Syrian Bʿath Party's chief ideologue until his death in 1968 (today it's Arsuzi, not Aflaq, who is celebrated as the founder of the Baathist movement inside Syria). Aflaq latched on to the Iraqi Baath Party, but that was moving away from his original vision too (although it continued to nominally adhere to Aflaq's ideology).
It's at this point that the term "Neo-Baathism" really becomes a thing, and although it has connotations of nationalism and Communism vs. Aflaq's pan-Arabism and socialism, what it really signifies is that the Baath Party, in both Syria and Iraq, simply became an ideological fig leaf for military dictatorship. The Iraqi and Syrian Baathist regimes didn't get along for the same reasons any other pair of military dictatorships might not get along: their respective dictators didn't like each other very much. Jadid, though he never took an office higher than #2 in the Syrian Baath Party, ran the country for over four years, during which time he steadily lost power to Assad. In 1970, he was thrown in prison when Assad finally decided to seize power for himself, and he spent over two decades there before he died in 1993.