"We announce our pledge of allegiance to the caliph Ibrahim Ibn Awad to listen and obey," the audio recording said, referring to IS leader Abu Bakr al-Baghdadi.
The group has waged a campaign of violence from its Sinai Peninsula stronghold that has killed scores of policemen and soldiers since the Egyptian army ousted Islamist president Mohamed Morsi in July last year. It had previously expressed support for IS, but stopped short of pledging its allegiance before today, even denying it last week.
Interior ministry spokesman Hany Abdel Latif told AFP the announcement would make no difference to Egypt's fight against the militants.
"They are just different names for the same terrorists," he said. Ansar Beit al-Maqdis, which means Partisans of Jerusalem, was formed during the security vacuum that followed the overthrow of longtime President Hosni Mubarak in the Arab Spring revolution of 2011.
The group has conducted cross-border attacks against neighbouring Israel, as well as attacks on Egyptian soldiers and police. It has said it wants to implement Islamic law, and avenge Islamists killed in the crackdown that followed Morsi's overthrow.