The military said the target was a "global jihad terrorist" linked to the April 17 rocket attack on Eilat.
"A man in his 20s was martyred and another injured in an Israeli air strike... In Shati refugee camp in western Gaza City," health ministry spokesman Ashraf al-Qudra told AFP.
It was the first deadly Israeli air strike since an Egyptian-brokered truce went into force on November 21, and the first targeted killing by Israel in Gaza since the eight-day conflict which that ceasefire ended.
The military confirmed Mishal was the target, saying he belonged to the Salafist group that claimed responsibility for firing two rockets at Eilat from the Egyptian Sinai.
"A global jihad-affiliated terrorist has been targeted by an IAF (Israeli Air Force) aircraft in the northern Gaza Strip in response to rocket fire towards Israel," the military said.
"On April 17, Mishal was involved in the (Mujahedeen) Shura Council organisation's firing rockets at Eilat," it added, without giving further details.
The Gaza-based council claimed the April attack, saying it was in "response to the continued suffering of the downtrodden prisoners in Israeli jails".
"Those who fired them are apparently a terror squad that departed Gaza and used the territory of Sinai to attack an Israeli city.
"We will not accept this and we will exact a price -- this has been our consistent policy the past four years and it will serve us in this case as well," he said in remarks relayed by his bureau.
He reiterated his warnings on Sunday morning, saying Israel would respond in "a very offensive way against any rockets or missiles" fired at the Jewish state.
Israel's Defence Minister Moshe Yaalon told public radio today that Hamas, which governs the Gaza Strip, "is trying to calm the territory, but it will not be calmed, and nor will we.
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