“A distinction must be made between bilateral relations and an international conference," Gul said on a visit to Tunisia, after a Turkish diplomat said Ankara had not decided whether to invite France to the conference.
The French parliament passed a law last year making denial that the Ottoman empire committed genocide against its Armenian population a criminal offence, infuriating Turkey.
France had already recognised the killings as a genocide, but the new law sought to go further by punishing anyone who denies this with up to a year in jail and a fine of 45,000 euros.
The French Constitutional Council labelled the law "unconstitutional," but President Nicolas Sarkozy promptly ordered his government to draft a new bill.
Gul called for wide international participation at the Istanbul conference, "including Russia," an ally of Bashar al-Assad's regime, which along with China boycotted the Tunis meet.
Gul and Marzouki both said they were opposed to any foreign intervention in Syria and stressed the need for a political solution.
Marzouki predicted that "sooner or later the regime will fall," while Gul said, "No regime can stay in power by oppressing its people in this manner."
The Tunisian president has offered asylum to Assad if it helps to bring peace to Syria after nearly a year of violence.
Meanwhile, Syria's deputy oil minister, Abdo Hussameddin, resigned on Thursday to join an anti-regime revolt, as UN-Arab League special envoy Kofi Annan urged a path of diplomacy rather than militarisation to end the crisis in Syria.
On the ground, another four civilians were killed in violence across Syria on Thursday, said the Syrian Observatory for Human Rights, which this week put the number of people killed since the uprising began a year ago at almost 8,500.