Somalia's transitional government is battling fighters from a number of armed opposition groups, including al-Shabab and Hizbul Islam, which have vowed to topple the administration of Sharif Ahmed, the president.
Abdi Mohamed Ahmed, who owns a tea shop in front of the Sahafi hotel, said about 10 fighters disarmed the hotel's guards on Tuesday morning and took the French nationals.
"The gunmen then sped away with their hostages," he said.
Several witnesses around the hotel, which reportedly also hosts several members of the Somali parliament, said some of the armed men were wearing government uniforms.
Mohamed Hassan Gafaa, the hotel manager, told The Associated Press news agency that the two men had registered at the Sahafi as journalists.
Kidnapping for ransom has been on the rise in Somalia for several years with aid workers and journalists most commonly targeted.
Two foreign freelance journalists - Canada's Amanda Lindhout and Australia's Nigel Brennan - have been held captive since August of last year.
No group has claimed responsibility for Tuesday's abduction, which came after a flare-up of violence in the capital over the weekend in which dozens of people were reported killed and at least 150 were injured.
Witnesses said fighters had retreated from areas around the presidential palace on Monday after several days of heavy fighting.