A decades-long border dispute in the Doumeira region that, on occasion, had turned violent, was dampened in 2010 when the two sides agreed to let Qatar mediate. Since then, 450 Qatari forces have been maintaining a buffer zone between the two sides – until they up and left last week.
Qatar offered no explanation for the move, though it comes amid a diplomatic dispute with other Arab nations, most notably the United Arab Emirates and Saudi Arabia, which have cut diplomatic ties and are now trying to isolate Qatar from the rest of the world. Saudi Arabia and its allies allege that Qatar supports Islamist extremists, a charge the small gulf nation denies.
Both Djibouti and Eritrea have good relations with Saudi Arabia and the United Arab Emirates, and have taken their side in the Gulf row.
Djibouti says that, in the absence of Qatari soldiers, Eritrea has once again occupied the disputed territory, and hints that military clashes are not out of the question.
Foreign Minister Mahamoud Ali Youssouf warned that Djibouti's military were "on alert" and said the nation has lodged complaints to the UN and the African Union (AU). The AU urged restraint and said it would send a fact-finding mission to the disputed border.
It’s possible that the disputed Doumeira region won’t be the only place where the troubles with Qatar will be felt.
"The Qataris are involved in a number of fields outside their immediate region,” H.A. Hellyer, senior non-resident fellow at the Atlantic Council in Washington DC, told FRANCE 24. "Many of those pressuring Qatar via these various measures are as well – and many times, they interact. There are probably very many arenas like the Djibouti-Eritrea scenario, and if this crisis in the GCC (Gulf Cooperation Council) continues we may see many more such abrupt disruptions."
Territorial tensions between the two Horn of Africa nations flared in 1996 and 1999, but the current crises dates back to 2008, when Eritrea sent its troops into the area, which lies north of the city of Djibouti and is strategically located at the entry to the Red Sea.
The dispute triggered several days of fighting that killed a dozen Djiboutian troops and wounded dozens. Eritrea had initially denied making any incursions, accusing Djibouti of launching unprovoked attacks.
After the UN Security Council requested both sides withdraw from the area, Qatar stepped in to mediate and deploy peacekeepers.
Diplomatic sources said Saturday that the UN Security Council would meet Monday afternoon in New York to discuss the crisis in a closed-door meeting requested by Ethiopia. The AU said it was "ready to assist Djibouti and Eritrea to normalise their relations and promote good neighbourliness within the framework of relevant AU instruments".
Djibouti is a close Western ally, hosts French and US military bases and is the main route to the sea for Eritrea's arch foe and Washington's top regional ally, Ethiopia.
Eritrea has fractious ties with the West, which had previously accused it of backing Somali and other regional insurgents. The government denies the charges.
Whether both parties are ready to negotiate is not entirely clear. In a statement issued Saturday, Eritrea did not directly respond to the allegations that it had invaded Djiboutian territory, saying only that the nation would not respond to "news – factual and speculative – churned out in the last few days".
"The government of Eritrea will make its views known when it obtains full information of the entire episode," said a statement issued by the information ministry in Asmara.
Djibouti has been more forthcoming. "Djibouti is a peaceful country and we have prioritised diplomatic solutions, but if Eritrea insists in seeking military solutions, Djibouti is ready for that," Youssouf said.