The command council of the rebel Free Syrian Army called for unity on Saturday after several prominent rebel brigades rejected the opposition National Coalition umbrella group.
The Supreme Military Council said it had decided to "issue a call for closing ranks, renouncing division, and... rejecting all kinds of dissension caused by trying to separate the political wing from the military one."
The statement came after 13 rebel brigades, including prominent groups that work with the Military Council, rejected the authority of the National Coalition -- the opposition's most prominent political institution.
Powerful brigades including Liwa al-Tawhid, Ahrar al-Sham and Liwa al-Islam joined the Al-Qaeda-affiliated Al-Nusra front in rejecting the Coalition, saying it "does not represent us, nor do we recognise it."
They did not make reference to the Syrian Military Council, which commands the mainstream Free Syrian Army as well as non-FSA groups cooperating with it.
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The Military Council statement reiterated "the need to respect institutions of the Syrian Revolution; primarily the Syrian Coalition."
The decision of the 13 brigades to reject the Coalition was seen by some as a response to increasing pressure on the grouping to participate in negotiations with the Syrian regime.
The international community has pushed for a peace conference in Geneva, but the opposition has said it will not negotiate unless President Bashar al-Assad leaves office.
The Military Council said it continued to reject "dialogue with the terrorist regime in Syria."
It said the "minimum acceptable" would be negotiations with Arab and Muslim states that adhered to Coalition conditions: "the need for Assad to step down, a transfer of power, and bringing to justice those who have committed war crimes against the Syrian people."
More than 115,000 people have been killed since the conflict in Syria began in March 2011, according to the Syrian Observatory for Human Rights, a monitoring group.