Muslim cleric Sheikh Hassan Dahir Aweys, who is also on a UN list of al-Qaeda associates, was named head of the Council of the Islamic Courts over the weekend.
Sean McCormack, the US State Department spokesman, said on Monday: "Of course we are not going to work with somebody like that and of course we would be troubled if this (choice) is an indicator of the direction that this group would go in."
Pressed whether this meant the United States would not deal with any member of the group in the future, he replied: "Let's wait, let's see what the collective leadership of this group does."
McCormack said there were a lot of "shifting sands" in terms of the leadership and composition of the Islamists and the United States was waiting to see what happened.
The Council of the Islamic Courts is a parliament for the Islamists, whose militias seized Somalia's capital Mogadishu from US-backed warlords on June 5 after months of fighting that killed at least 350 people.
Sheikh Sharif Ahmed, the moderate face of the courts, was named head of an executive committee in charge of the courts' administration, which will implement the parliament's decisions.
The rise of Aweys has alarmed the United States, which fears the Islamists want to establish Taliban-style rule in Somalia, despite repeated denials by Ahmed.
Asked whether the United States would push for the arrest of Aweys should he, for example, attend international meetings to discuss Somalia, McCormack said he did not know the legal status for anyone on the list.
"Of course we are not going to work with somebody like that and of course we would be troubled if this (choice) is an indicator of the direction that this group would go in"
US State Department spokesman
McCormack said the United States had not yet had any formal meetings with the Islamists, except for a brief encounter between a US diplomat in Sudan's capital Khartoum for meetings and one of the Islamists.
"It wasn't a meeting that was set up in advance. It was a chance encounter," he said.
The US move came on the same day that the Islamists said in Mogadishu they would stone to death five rapists. McCormack made no comment on these planned executions.