The Polisario Front are fighting Africa's longest running territorial dispute for the separation of the Western Sahara from Morocco, which claims the region.
The UN negotiated a ceasefire in 1991 and a third round of talks are due in January 2008 between the two sides.
Sources close to the government expressed surprise at Rabat's decision to withdraw its ambassador as Baudin, who is a member of the Socialist Party, is not part of the Senegalese government.
"The recall of the Moroccan ambassador to Senegal is an unfriendly gesture towards the Senegalese people ... and Senegal, while waiting for clarification, is calling back its ambassador in Morocco for consultation," an official statement, released in Dakar, said.
Senegal has maintained cordial relations with Morocco. The Senegalese Democratic Party (PDS) of Abdoulaye Wade, the Senegalese president, which took power in 2000, has supported Morocco's offer of autonomy for the Western Sahara.
Some strains in the relationship have emerged recently, with the Senegalese government re-taking control of Air Senegal, the national airline, from Morocco's Air Maroc after what it said were heavy financial losses.