From the beginning, it made strategic sense for Israel to provide military aid to rebels in South Sudan. This would serve as a useful distraction to Egypt and Sudan, and would open a new and vulnerable front against the Arab World. However, it wasn’t until the June 1967 war that Israel truly acted upon this opportunity, following Khartoum’s decision to support Egypt in that conflict.  Joseph Lago, then the leader of the South Sudanese Anya-Nya ("Viper Venom") guerrilla organization, appealed desperately to Israel, asking it to help in preventing integration of Sudanese units within the Egyptian army by pinning them down in an ongoing conflict with the fighters of South Sudan. This would carry a number of advantages for Israel, including strengthening Israel’s operational connections with Kenya and Ethiopia, which were states within Israel’s geo-strategic ‘second circle.’ Providing such aid would also carry moral weight: Israel would help a nation struggling for independence against what south Sudanese felt to be Islamic “tyranny.”
The deep empathy that many South Sudanese feel for Israel has a number of sources. For many Evangelical Christians in South Sudan, the Bible represents a major – if not the main – source of inspiration. In this instance, Israel is not only the Holy Land but also the only country in the world which provided help to South Sudan in its hour of need.  It goes without saying that Israel welcomed this way of thinking, not only because of its ‘periphery policy’ but also, later on, because of close personal relations that developed with the South Sudanese people. This article will explore the development of ties between Israel and South Sudan to the present time.
The initial connections between representatives of Anya-Nya and Israel
Fighting between the northern and southern regions of Sudan began as early as 1955, a year before Sudan’s independence from Egypt and Great Britain. Ultimately, the ongoing conflict would wreak a terrible human cost: over 2 million people died and 4 million were displaced from their homes as refugees or IDPs. The regime mobilized militia forces, known as the Murahilun, to raid southern villages. These raids often resulted in the robbing, killing, and sexual assault of non-combatant civilians. In response, the southerners established Anya-Nya, but without much success in combat. At that point they unsuccessfully requested help from any international actor who might be willing to provide it. After 1961, these appeals were directed at Israel as well. 
As noted above, Israel decided to actively provide support following the Six Day War of June 1967. This support was most notable during the latter part of the first phase of Sudan’s civil war (1956-1972), where support included not only moral backing and diplomatic assistance but also more tangible aid, such as arms, materiel, and access to oil and other desperately needed natural resources.
Relations Develop: 1968 to South Sudan’s independence
Under the rule of President Ja'afar al Numayri (1969-1985) the South was discriminated against, and many of its people were placed on the brink of starvation. From 1972 to 1983, following the Addis Ababa Agreement, there was a break in the civil war. Consequent to this, relations between the South and Israel weakened but remained intact.
The second round of the civil war began in 1983, following the Numayri regime’s decision to enforce Shari’a law on the south. In the wake of the renewal of fighting, the Anya-Nya movement changed its name to SPLM (Sudan People’s Liberation Movement), with its military arm, the SPLA (Sudan People’s Liberation Army), led by John Garang de Mabior. Garang's vision was that the South under him would lead a united Sudan as a democratic, pluralist State. Garang also strengthened relations with Israel.
A number of factors enabled the South to reconquer the town of Kormuk. These included regional pressures exerted by Egypt and Libya on the Khartoum government and the 1989 coup d’etat led by Omar al-Bashir. Also that year, tensions were sharpened both internally and regionally, following the Islamist Revolution led by Omar al-Bashir and Hassan al-Turabi. The 1990s also witnessed Sudan’s cooperation with Osama bin Laden’s al-Qaeda. Hassan al-Turabi, who was a significant proponent of Sudan’s Islamist revolution, claimed that all that was needed for the spread of Islam throughout Africa was the defeat of South Sudan. Following the 9/11 attacks in New York and Washington, the al-Bashir regime began cooperating with the United States in its War on Terror. As the South Sudanese had been able to attract much sympathy in American public opinion, new pressures were put on the Government of Sudan and SPLM leaders to reach an agreement. Thus, the Comprehensive Peace Agreement (CPA) between the two parties was signed in 2005, which paved the way to South Sudan’s independence in July of 2011.
In 2005, SPLM leader Garang was killed in a helicopter crash while returning from Uganda. Garang's successor, Salva Kiir Mayardit, favored pursuing independence for South Sudan, and maintained the relationship that Garang had enjoyed with Israel.  Following independence, Israel was one of the first countries to extend diplomatic recognition to the newborn state. In turn, President Kiir’s first official diplomatic visit was to Israel. 
Unfortunately, peace did not last long. In December 2013, shortly after South Sudan’s independence, a civil war erupted in the newborn nation, with devastating humanitarian effects. As a result, many international development and assistance projects, including those led by Israel, were put on hold.
The reciprocal strategic importance of South Sudan and Israel was the basis of long-standing relations that have persisted from the late 1960s to the present time. During the many decades of civil war in Sudan, Israel saw South Sudan as a potential ally in an otherwise hostile Arab-Muslim regional neighborhood. South Sudan, for its part, viewed Israel as not only a potential source of military assistance but also as a moral partner.
This reality has changed over the last few years. Al-Turabi died in 2016, and the al-Bashir regime faces significant economic difficulties alongside ongoing social and political unrest. South Sudan is still mired in continuing conflict, with grave consequences both domestically and regionally. Meanwhile, Israel is developing a new policy of rapprochement towards the Sahel states of Africa.
All of these changes demand a reassessment of future Israeli policy towards South Sudan. The hope remains that, despite the challenges which South Sudan is facing, Israel and other countries will succeed in helping South Sudan help itself.
Haim Koren is a former Israeli ambassador to South Sudan and Egypt.
 David Ben-Uziel, A Mossad Agent in Southern Sudan, 1969–1971: An Operation Log. (Hertzliya: Teva-Hadvarim, 2017).
 Haim Koren, "Sudan’s Policy in the Era of Arab Upheaval: For Good or for Evil?" BESA, Bar Ilan University, April 13, 2018.
 The ‘Periphery Policy’ (or strategy) refers to Israel’s search for non-Arab or non-Muslim allies in the greater Middle East and African regions. For more information, see Michael Bar Zohar, "David Ben-Gurion and the policy of the Periphery 1958: Analysis", in Itamar Rabinovich and Jehuda Reinharz(eds.) Israel in the Middle East: Documents and Readings on Society, Politics and Foreign Relations, pre- 1948 to the Present. (Waltham, Mass: Brandeis University Press, 2008), 191-197; Noa Schonmann, "The Phantom Pact: Israel's Periphery Policy in the Middle East", Ph.D. Dis. University of Oxford, 2009.
 Joseph Lagu, Sudan Odyssey Through a State: from Ruin to Hope, Khartoum, 2006.
 O.M. Beshir, The Southern Sudan: Background to Conflict, Khartoum, 1970; Joseph Oduho and William Deng, “The Problem of the Southern Sudan,” International Affairs 40, no. 1 (January 1964): 152-153.
 Yotam Gidron, “One People, One Struggle’: Anya-Nya Propaganda and the Israeli Mossad in Southern Sudan, 1969–1971,” Journal of Eastern African Studies 12, no. 3 (2018): 428-453.
 Ben-Uziel, 2017.
 Irit Back, John Garang's Vision for a "New Sudan" – A Contemporary Perspective, Ifriqiya (July 2016) [in Hebrew].
 Haim Koren, South Sudan in the 'Identity Thicket' - Challenges to building a nation-state, Ifriqiya (July 2015).
 "South Sudan President Visits Israel for First Time," Reuters, December 20, 2011.