They are in essence one and the same.
From its humble beginnings, the Baath Party now controls two countries and over 20% of the world's oil resources. The leaders of its two largest wings are known to dislike each other intensely, but share many common goals, and a vision of an Arab world marching together under the banner of "Unity, Freedom, and Socialism." Although the Baathist governments of Syrian President Hassad and Iraqi President Hussein have been known to support Islamic militants when it suited them, they are widely loathed and considered as infidels by many Islamic fundamentalists If the Baath Party is uncompromising in its secular viewpoint, it is equally uncompromising in its dislike of the West and its hatred for "Zionist colonialism in occupied Palestine."The three major proponents of early Baathist thought, Zaki al-Arsuzi, Salah al-Din al-Bitar, and Michel Aflaq, were middle-class educators whose political thought had been influenced by Western education. At first they expounded their visions of pan-Arabic nationalism to small audiences; by 1947 they had established a constitution and a party headquarters in Damascus. After 1948, many blamed the founding of the new State of Israel on Arab disunity. By 1954 the Baath Party was established in Iraq; by 1963 it had come to power in both Iraq and Syria.
Still, there were major differences between the Syrian and Iraqi vision of "pan-Arabic unity." Hafez Assad, who came to power in a 1970 coup, was an Alawite, a member of a sect whose practices are largely influenced by Shi'a Islam but which include borrowings from Christianity, Gnosticism, Mithraism and pre-Islamic pagan practices. He saw religious fundamentalism as a threat because he had witnessed first-hand Sunni persecution of Alawites. (Assad had come to power in the Syrian army because the military was one of the few opportunities open to Alawites: much as African-Americans make up a disproportionate percentage of U.S. soldiers, a significant number of Syrian soldiers were Alawite). The Iraqi Baath Party, in contrast, was made up largely of Sunni Moslems. While Assad was courting Iran and trying to present the Alawites as Shi'a Moslems, Iraq's Sunnis were trying to cement their hold on power over Iraq's majority Shiite population. (There has historically been tension between the two sects; this lessened somewhat during the Iran-Iraq War, when Iraqi Shi'ites remained loyal to the Iraqi government despite fears they would support Iran).
These conflicts only intensified when Sadaam Hussein assumed control of the Iraqi Baath Party, and the Iraqi government, in 1979. His expansionist ideas led to a decade-long conflict with Iran… a conflict in which Syria backed Shi'ite Iran against Baathist Iraq. This led the two countries to sever relations, and began a long period of mutual hostility. Each regime sought to portray itself as the legitimate representative of Arab unity, while supporting dissidents against their opponent. When Hussein invaded Kuwait in 1990, Syria was among the Arab states who sent troops to participate in "Operation Desert Storm." Only in 1997 would a rapproachment between the two Baathist parties begin; since Assad's death in June of 2000, relations have improved considerably.
Hafez Assad's successor, his son Bashir, has encouraged entrepreneurial ventures and free trade; he has also made overtures toward the United States and toward the World Bank. Following in his father's footsteps, Assad has also continued to play one end against the other, currying favor with the Iranians and also working toward improving Iraqi-Syrian relations. Syria has been one of the key players in helping Iraq evade U.N. sanctions; it is estimated that some $15 million of Iraqi oil is smuggled through Syria weekly, providing a lucrative trade for both cash-starved governments.
Despite the lip service paid to "freedom," both branches of the Baathist Party have a dismal human rights record. Their commitment to "Socialism" has not stopped either Hussein or Assad from establishing dynastic dictatorships, nor has their commitment to "Arab Unity" stopped them from ruthlessly crushing those Arabs they saw as opponents. Nevertheless, the Baathist movement remains popular in many Arab countries, where Hussein is seen as an underdog standing up against Western imperialism. A large-scale invasion of Iraq, or a war between Syria and Israel, could well result in the Baathists becoming even more popular on the Arab street.
-- Article at Hybridmagazine.com