The president on Saturday issued a statement saying he and his wife, Michelle, congratulate Muslims in the U.S. and around on the world on a "blessed day."
Obama said even at this festive occasion, Muslims remember the less fortunate, those suffering in poverty, hunger, conflict and disease.
In her own statement, Secretary of State Hillary Rodham Clinton said the occasion is a reminder that the values of Islam -- "charity, community, cooperation, compassion are values which we hold dear as Americans."
Obama also used a Rosh Hashana message to renew his call for peace between Israel and its Arab neighbours.
Rosh Hashana began at sundown on Friday and Obama said in a video message released Thursday that the Jewish new year should be a time of prayer and celebration.
Obama said the holy day should be an opportunity to heal old divisions and seek new understandings. He said he wants to bring lasting peace to Israel so future generations will have a safe existence.
He also said it is time to reject anti-Semitism, which he says is too prevalent in the world.
The message was recorded in English but includes subtitles in French, Hebrew, Russian, Spanish, Turkish, Arabic and Farsi.