Mohamed Zaouari, 49, was killed in a hail of bullets at the wheel of his car outside his house in Tunisia’s second city Sfax in December 2016.
“The two people who carried out the assassination were identified — both were of Bosnian nationality,” prosecution spokesman Sofiene Sliti said.
One of the suspects was arrested on March 13 in Croatia, he said, without giving details on the other individual.
The government earlier confirmed that “foreign elements” had been involved in the killing of the Tunisian-Belgian citizen, which sparked outrage in Tunisia.
Shortly after his death, Hamas said he was a drone expert who had worked for the “resistance” for a decade before being killed by “Zionist treachery”.
Israel refuses to respond to such allegations.
Israel has fought several wars with Hamas, which rules the Gaza Strip, as well as assassinating several of the Islamist movement’s members in the past.
In November 2017, Zaouari’s family denounced “silence” on the part of the authorities and called on them to provide more details on the investigation into his killing.
Israel was also accused of being behind the assassination last month in Malaysia of Fadi al-Batsh, a Hamas scientist who was said to be a rocket-making expert.
Family and friends of Batsh accused Israel’s Mossad spy agency of carrying out the killing in Kuala Lumpur on April 21.