Israel has been renewing links with the south, as the Jewish state, increasingly isolated internationally, seeks to forge new alliances in Africa, Asia and the Balkans.
At the same time, the leaders of the Iranian-backed fundamentalist Palestinian movement Hamas, which rules the troubled Gaza Strip on Israel's southern border, have been cozying up the Muslim regime of President Omar al-Bashir in Khartoum.
With Islamic parties making giant gains in free parliamentary elections across North Africa amid the Arab Spring, Israel is scrambling to find new friends in the region, the Mediterranean and Africa.
The 2010 rupture of relations between Israel and a key non-Arab ally, Turkey, has heightened the Jewish state's sense of isolation at a time when it sees an existential threat from a nuclear-armed Iran.
Israel's emerging relationship with predominantly Christian South Sudan, which became independent of Khartoum's rule in July 2011 after decades of civil war, was marked by a December visit to the Jewish state by Salva Kiir, the former separatist leader who's now president of the world's newest state.
Israel recognized the Republic of South Sudan within hours of its independence.
The Jewish state's ties with southern Sudan go back to the Anyanya rebellion in the 1960s when it covertly provided arms shipments and military training to the guerrillas.
By doing so, Israel sought to pin down the Arab Muslim regime in Khartoum and prevent it deploying Sudanese troops to support Egypt along the Suez Canal after the 1967 war.
Israel continued to aid southern separatists over the years that followed when Sudan supported Islamic fundamentalists, including the late Osama bin Laden.
Kiir, wearing his signature black Stetson hat, was accompanied by his defense and finance ministers during his visit to Israel, during which he was feted by Prime Minister Binyamin Netanyahu and Defense Minister Ehud Barak.
Kiir reportedly requested Israeli help in technology, agriculture and water. Israeli sources said he also discussed military cooperation.
There has been no public indication of a formal defense agreement but it is likely that Israel's intelligence service, the Mossad, and Military intelligence will upgrade their long-time presence in South Sudan.
Khartoum has long been involved in supporting militant anti-Israel groups and in recent years has been a conduit for Iranian arms shipments into Egypt en route for Hamas militants in Gaza.
"Nobody will talk about security cooperation, which is obviously something that the South Sudanese, already involved in skirmishes with Sudan, have in mind," The Jerusalem Post reported.
"It is a friendly country in the heart of a region that Iran is trying to penetrate. Israel is concerned about a flow of arms going from Iran, through Sudan, into Egypt, Sinai and then Gaza."
Israeli warplanes were reported to have destroyed two arms convoys crossing Sudan's northern desert in January 2009, while the navy seized shipments in the Red Sea.
In November 2011, Israeli aircraft were reported to have attacked trucks in the Wadi al-Allaqi region of northern Sudan near the Egyptian border. Another Israeli raid reportedly took place Dec. 15. The Sudanese media said Israeli Apache helicopter gunships landed near a Sudanese radar installation.
There have even been reports of Israeli submarines off Sudan's Red Sea coastline.
Iran has been making diplomatic inroads into Africa of late, so establishing an intelligence-military presence in South Sudan would clearly be advantageous to Israel, particularly at a time when East Africa looks like it's headed for an oil boom.
Meantime, South Sudan is locked in a potentially explosive dispute with Khartoum over oil resources along the border between the two states. Most of these lie in the south but the only export pipeline runs across the north to Port Sudan. Khartoum recently seized large southern oil shipments, sharpening tensions.
While Netanyahu and Kiir were courting each other, Hamas leaders have been in Khartoum seeking financial support for Gaza, which is under Israeli economic blockade, and recognition of Jerusalem as capital of a Palestinian state.
Hamas' political leader, Khaled Meshaal, arrived in Khartoum Dec. 27 and was later joined by Gaza Prime Minister Ismail Haniya.
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