Marzouki pardoned the convicted criminals Tuesday in what has become an annual tradition in Tunisia, Tunisia Live reported.
However, attention has been drawn to the names of several inmates who were not pardoned, including rapper Ahmed Laabidi and blogger Jabeur Mejri.
Laabidi, known by his stage name Kafon, was arrested in June 2013 for using marijuana and sentenced to one year in prison and a $600 fine.
Ghazi Mrabet, Laabidi's lawyer, said his client has not had a proper trial.
"I literally had to dig his file from the archives," Mrabet told Tunisia Live. "He spent seven months in jail without any legal representation. So far no date for a trial can be set until his case gets transferred to the appeals court in Tunis."
"Legally speaking, Kafon couldn't have possibly enjoyed the presidential amnesty since he has had no trial and his file case was stuck in the Ben Arous court due to administrative obstacles," he added.
The rapper's case did not receive much media attention until his song "Houmani" became a hit, Tunisia Live said.
"At first only close friends of Kafon and some alternative media spoke of his arrest," Azyz Amami, an activist and member of Kafon's support committee, told Tunisia Live. "Later on, official channels such as Nessma and Tunisian national television developed an interest in the story, but only when Kafon himself grew to fame."
Meanwhile, blogger Mejri was sentenced to seven and a half years in prison on March 22 for posting cartoons of the Prophet Mohamed online.
His lawyer, Ahmed Mselmi, told Tunisia Live he has filed two amnesty requests and that only Marzouki has the power to pardon his client. The president has previously said that he intends to pardon Mejri, but is waiting for "right political moment."
"The difference between Kafon and Mejri is that in Mejri's case there was already an appeal which makes the question of a pardon possible," Mrabet told Tunisia Live.