There are hundreds of groups. Here are the main coalitions
Since last week the Syrian ceasefire deal been in full effect. Despite repeated violations during this week, world leaders commit to putting their faith in this temporary truce.
The Syrian ceasefire does however not cover the Islamic State of Iraq and the Levant (ISIL) and Jabhat Al-Nusra, the Syrian Al-Qaeda branch, and other designated terrorist groups. Despite the global powers making this statement, it remains unclear who these “other designated terrorist groups” actually are, it is therefore safe to say that no one really has an idea, since it has been rather clear that the main actors of this conflict differ radically in that designation.
It is estimated that over 100 rebel groups participated at the implementation of this truce deal, with more joining as Russia has been ramping up its efforts of reconciliation in Syria.   Different actors consider different fighting parties to be terrorists and conflicting interests makes the matter even worse.
While it is difficult to keep track of the estimated 1500 rebel groups fighting on the ground, it has never been a secret that the main rebel factions, Jabhat Al-Nusra, Jaysh Al-Islam, Harakat Ahrar-Al Sham and the Free Syrian Army have cooperated, carried out joint missions, and have occupied towns and villages together against the Syrian Armed Forces.    These groups intermingle deeply and make it rather difficult for outside observers to distinguish between.
The main areas of the truce deal are implemented in the southern and central parts of the country, with several pockets of rebel held areas, besieged for some years now, being able to catch a breath. Below is a map showing the rather small areas considered to be “green zones” for the truce.
Groups and areas part of the ceasefire deal or with unclear status
The ceasefire deal covers a few specific areas, namely the southern Daraa province where several rebel groups part of the “Southern Front Brigades” have agreed to several reconciliation and truce deals.  The ceasefire is also supposed to cover the northern Homs/southern Hama pocket of rebel resistance where Russia and government forces have come under scrutiny for bombing. Despite all of this, there’s no denial of the heavy Nusra and Harakat Ahrar Al-Sham presence in the towns of Talbiseh and Al-Rastan.   
Also, the ceasefire was violated several times amid a new Islamist offensive launched six days ago. 
Other participants of the truce are the Kurdish YPG forces and their allies from the Syrian Democratic Forces (SDF) who have pledged to abide by the truce despite Turkish insistence on their exclusion. 
Southern Front Brigades
Leadership: Gen. Bashar al-Zoubi (Alleged)
A coalition of 58 militant group factions associated with the Free Syrian Army was formed in February of 2014. The groups has recieved US and western backing in the form of training and arms. 
Despite its name, there remains heavy dispute over their association with the Free Syrian Army at all.
The Carter Center, a private organization in the U.S. in February 2015 also described ‘The Southern Front’ as a loose coalition of self-described moderate armed groups without leadership or organizational structure, that has agreed on the name ‘Southern Front’ to receive support from the ‘Friends of Syria’ “an international diplomatic collective, which focuses on supporting the Syrian opposition”
The Southern Front Brigades have made it no secret that they cooperate with Jabhat Al-Nusra in this area as well, with the groups launching multiple offensives together against the Syrian Armed Forces.
YPG & Syrian Democratic Forces
Leadership: Sipan Hemo
The People’s Protection Units (YPG) were introduced to the Syrian conflict rather late, with their first clashes occurring during the summer of 2012 where Kurdish forces assumed control over Kobani and Afrin among other areas.   The Kurdish campaign has mostly focused on fighting Islamists from Jabhat Al-Nusra and Islamic State of Iraq and the Levant since then, with the most heated battles taking place around Kobani and Tal Abyad. The Kurdish effort has since long been supported by the US led anti-ISIL coalition with regular airstrikes backing up YPG forces. The Turkish government however views this group as a Syrian branch of the Kurdish separatist PKK group in Turkey. Thus Turkey views this group as a threat and has been shelling them several times. 
The Syrian Democratic Forces is a relatively new alliance of Kurdish, Arab and Assyrians militias formed in October 2015. The YPG forms the biggest group participating. 
The alliance has shown tendencies to tolerate Syrian government forces and vice versa with President Bashar al-Assad stating that he is willing to make concessions and engage in talks with them. Since the start of the Russian intervention in Syria, the SDF have also engaged in cooperation and talks with Russia.  
Operations rooms/Alliances not included in the ceasefire deal
A conglomerate of over a dozen Islamist militant groups who formed the Ansar Al Shariah coalition in 2015 to combat government forces in Aleppo. The forefront groups participating in this coalition are Jabhat Al-Nusra, Harakat Ahrar Al-Sham, Jabhat Ansar Al Din and the Syrian Turkmen Brigade. Because of Al-Nusra being heavily funded and armed by Saudi Arabia and Turkey among others, it is likely that the other members of the coalition have access to and enjoy the same kind of backing.
Another coalition of Islamist militants in Aleppo, totalling up to 50 groups and formed in 2015, with a similar goal “to “liberate” Aleppo City from the Syrian regime”. Predominantly composed of fighters from the large hardline Harakat Ahrar Al-Sham group and Jaysh Al-Islam. Also composed of more than a dozen FSA units as well, It is noticeable that Jabhat Al-Nusra is not part of this operations room.
Jaysh Al- Fateh (Army of Conquest)
Formed in March of 2015, this alliance was a special joint Saudi/Turkish project which was aimed at expelling the Syrian Arab Army from the Idlib Governorate.  The Army of Conquest quickly captured the remainder of the Idlib Governorate that was under government control, including Idlib City, while also besieging the two predominantly Shia towns of Kafraya and Al-Fuaa. The alliance was originally formed by seven founding groups, of which three were direct Al-Qaeda affiliates (Harakat Ahrar Al-Sham, Jabhat Al-Nusra and Jund Al-Aqsa) and who provided more than 90 % of the troops.  Several other groups such as Sham Legion (Faylaq Al-Sham) are Muslim Brotherhood affiliates. Interestingly enough, this coalition also had the Turkestan Islamic Party, a Islamist separatist organization founded by Uyghurmilitants in western China and is now proudly displaying its fighters in Syria.  It is widely believed that Turkey and specifically Turkish intelligence has provided aid to this terrorist organization. 
Leadership: Mohammed Shakerdi 
Formed in January of 2014, the Army of Mujahedeen was formed out of several smaller FSA and Islamist brigades, notably the Harakat Nour Al-Din Al-Zenki Islamic Brigades and the Al-Noor Islamic Movement. In 2015, with the formations of several other alliances, the prominent Harakat Nour Al-Din Al- Zenki group left the alliance. Foreign support has been given through the United States and Qatar among others.  The group mainly operates in the Aleppo Governorate, but claims to also operate in Idlib.
Main terrorist groups not included in the ceasefire deal
These four main groups fighting the Syrian Armed Forces are considered by the Syrian, Russian & Iranian governments to be terrorist organizations that are not included in any truce or ceasefire deal.
Islamic State of Iraq and the Levant (ISIL)
Leadership: Abu Bakr Al-Baghdadi
Local type of leadership: Wilayah & Emirs
A Salafi Takfiri militant group with origins from Iraq. ISIL has today grown into arguably the most powerful militant group fighting in the Syrian war with estimates ranging between 52,000–250 000 in terms of manpower. ISIL controls large parts of eastern Syria and sizeable portions of central and northern Syria. ISIL entered the Syrian war in April 2013 after having wreaked havoc in neighbouring Iraq for years before, and quickly began to gain strength in Syria, capturing several areas in northern Syria. ISIL began as an ally to the various rebel groups operating in northern Syria, including Jabhat Al-Nusra and the Free Syrian Army. This alliance culminated in the capture of the Menagh Military Airbase in the Aleppo Governorate, in August 2013. 
Internal divisions within the different Al-Qaeda branches of Jabhat Al-Nusra and ISIL on one hand and ISIL and the other rebel groups on the other, sparked a rivalry that culminated in a inter-Islamist conflict on New Years eve of 2013. Since 2014, ISIL has not only been fighting the government of Syria and the Kurdish YPG, but also other terrorist organizations in a power struggle for domination of Syria. ISIL currently controls 35-40 % ( 1.5 -2 million people) of the country and one provincial capital in Syria: Raqqa city.
Leadership: Abu Muhammad Al Golani
Strength: ~10 000-15 000
Main external backers: Turkey & Saudi Arabia
Area of operations: Mainly in the Idlib Governorate, which is also a stronghold of Al-Nusra and their allies. Nusra also enjoys strong support from the local population in some of these areas.
The Al Nusra Front, Al-Qaeda’s official branch in Syria. Established in 2012, Jabhat Al-Nusra quickly took a leading role in the battle against government forces. By the second half of 2012, Jabhat al-Nusra stood out among the array of armed groups emerging in Syria as a disciplined and effective fighting force. Jabhat Al-Nusra, unlike many of the other rebel groups, operates through almost the entire country, with branches spread out across Idlib, Aleppo, Latakia, Homs, Hama, Daraa and Damascus. Several sources put their manpower strength at somewhere between 10 000- 15 000 active militants, with more recruits joining from Turkey, who together with Saudi Arabia form the main external backers of this Islamist group. 
Jaysh Al-Islam (Army of Islam)
Leadership: Zahran Alloush (former)
Jaysh Al-Islam, formerly known as Liwa al-Islam is a Islamist/Salafist group formed in 2013 by the late Zahran Alloush, son of Saudi-based religious scholar Abdullah Mohammed Alloush. Jaysh Al-Islam primarily operates in the Damascus Governorate, mainly in the East Ghouta area. The group shares many ideological similarities to Al-Qaeda and other Salafist Takfiri organizations, with its now deceased leader Zahran Alloush being famous for his sectarian remarks against Shiites on several occasions. 
Jaysh Al-Islam have themselves claimed on May 2015 to have between 17 000-25 000 members, but this number is likely lower due to heavy casualties in recent battles. Jaysh Al- Islam controlled East Ghouta is not part of the ceasefire deal since they are considered to be Al-Qaeda affiliates, in close cooperation with Jabhat Al-Nusra
Harakat Ahrar Al-Sham
Arguably the largest Islamist rebel group in Syria and together with Jabhat Al-Nusra form the bulk of the Islamist rebels fighting the government in mainly Idlib, Latakia, Hama and Aleppo. Already in 2013, the group was said to have up to 20 000 fighters The group shares the same radical Wahhabi/Salafi ideology and have on occasions been thought to be a political front for Jabhat Al-Nusra, as this group is not a designated terrorist organization by the Security Council. The group enjoys heavy backing from Turkey and Saudi Arabia.  Harakat Ahrar Al-Sham is however not part of the ceasefire deal since they intermingle with Jabhat Al- Nusra on the same fronts that are not part of the agreement. This makes them legitimate targets according to the ceasefire deal.
Source: The Vineyard of the Saker