The pontiff made the comment in a message to the Patriarch of the Ethiopian Coptic Orthodox Church, H.H. Abune Mathias, to share his condolences.
The Pope said: "This year, our joy, which never fails, is eclipsed by profound sadness."
"I know that your Holiness is suffering deeply in heart and mind, in view of your faithful, killed for the sole reason of being followers of our Lord and Saviour Jesus Christ.
"I address my heartfelt spiritual solidarity to you, to assure you of my closeness in prayer amid the ongoing martyrdom being inflicted in so cruel a manner upon Christians in Africa, in the Middle East and in some regions of Asia.
"The blood of our Christian brothers and sisters is a testimony which cries out to make itself heard by all those who still know how to distinguish between good and evil... [which] must be heard above all by those who hold the fate of the peoples in their hands."
Islamic State's video appeared to show them behead 15 Ethiopian Copts on a beach, and shoot 15 others in the head in a desert.
It described them as "followers of the cross from the enemy Ethiopian Church".
In February, Islamic State posted a video showing them kill 21 Egyptian Coptic Christians.