In May 2009, the Department of State again certified Eritrea as a country that is "not cooperating fully" with U.S. antiterrorism efforts. The lack of Eritrean cooperation has constrained the ability of the United States and international partners to counter terrorist groups in the Horn of Africa and Somalia, particularly with respect to al-Shabaab leaders linked to al-Qa'ida. In late 2009, the UN Security Council created a sanctions regime on Eritrea that includes a territorial arms embargo and an asset freeze, travel ban, and arms embargo for those individuals and entities listed by the UN Somalia Sanctions Committee.

The Government of Eritrea has provided safe haven to political officials aligned with the now obsolete Alliance for the Re-Liberation of Somalia (ARS), including U.S. designated terrorist Sheikh Hassan Dahir Aweys, who resided in Asmara until May but is now in southern Somalia leading a faction of Hizbul Islam.

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