Jonah (Yunus): A Prayer From the Depths

Some prayers are long and eloquent. The most famous prayer of Jonah (peace be upon him) is just a single line — whispered in the deepest darkness a human being could imagine. Jews, Christians and Muslims all know Jonah’s story, and in all three traditions it is a story about second chances: for a reluctant prophet, and for a whole city.

A prophet who left too soon

The Qur’an names Jonah among the messengers and calls him Dhun-Nun, “the man of the fish”. He was sent to a large community — the Qur’an mentions a hundred thousand or more (Qur’an 37:147) — whom tradition places at Nineveh, as the Bible does. His people rejected his call, and Jonah left them in anger, before God had given him permission to leave.

The Qur’an tells the next part briefly. Jonah ran to a fully loaded ship; lots were drawn, apparently to lighten the vessel, and Jonah lost. He was thrown into the sea, and a great fish swallowed him (Qur’an 37:139-142).

Darkness upon darkness

Muslim commentators describe Jonah as being in layers of darkness: the darkness of the night, of the sea and of the belly of the fish. There, with nothing left but God, he called out:

وَذَا ٱلنُّونِ إِذ ذَّهَبَ مُغَٰضِبًۭا فَظَنَّ أَن لَّن نَّقْدِرَ عَلَيْهِ فَنَادَىٰ فِى ٱلظُّلُمَٰتِ أَن لَّآ إِلَٰهَ إِلَّآ أَنتَ سُبْحَٰنَكَ إِنِّى كُنتُ مِنَ ٱلظَّٰلِمِينَ ﴿٨٧﴾ فَٱسْتَجَبْنَا لَهُۥ وَنَجَّيْنَٰهُ مِنَ ٱلْغَمِّ ۚ وَكَذَٰلِكَ نُۨجِى ٱلْمُؤْمِنِينَ ﴿٨٨﴾

⁸⁷And [mention] the man of the fish, when he went off in anger and thought that We would not decree [anything] upon him. And he called out within the darknesses, "There is no deity except You; exalted are You. Indeed, I have been of the wrongdoers." ⁸⁸So We responded to him and saved him from the distress. And thus do We save the believers.

His prayer has three parts, and each one teaches something. He begins by affirming that there is no god but God. He then declares God free of any injustice or fault. Finally, he takes responsibility for himself and blames no one else. He does not even ask directly to be rescued. He simply turns back to God, and God answers.

The Bible likewise says: “Then Jonah prayed unto the LORD his God out of the fish’s belly” (Jonah 2:1, KJV). The heart of the story is the same: a servant who turned back to God in his lowest moment, and a God who heard him.

The Qur’an adds that if Jonah had not been one of those who constantly glorified God, he would have remained in the belly of the fish until the Day of Resurrection (Qur’an 37:143-144). His habit of remembering God in good times stood by him in his darkest hour.

Saved, sheltered and sent back

God caused the fish to cast Jonah onto an open shore. He was weak and ill, so God made a gourd plant grow over him for shade and nourishment (Qur’an 37:145-146). Then Jonah returned to his people — and something remarkable had happened. They had believed.

فَلَوْلَا كَانَتْ قَرْيَةٌ ءَامَنَتْ فَنَفَعَهَآ إِيمَٰنُهَآ إِلَّا قَوْمَ يُونُسَ لَمَّآ ءَامَنُوا۟ كَشَفْنَا عَنْهُمْ عَذَابَ ٱلْخِزْىِ فِى ٱلْحَيَوٰةِ ٱلدُّنْيَا وَمَتَّعْنَٰهُمْ إِلَىٰ حِينٍۢ ﴿٩٨﴾

Then has there not been a [single] city that believed so its faith benefited it except the people of Jonah? When they believed, We removed from them the punishment of disgrace in worldly life and gave them enjoyment for a time.

In many Qur’anic stories, a people reject their prophet and face the consequences. Jonah’s people are the great exception: they turned to God in time, and the punishment was lifted. Their story shows that it is never too late for a community, just as it was not too late for Jonah himself.

A prayer for every believer

Jonah’s prayer did not stay in the past. The Prophet Muhammad ﷺ taught Muslims to use it whenever they are in distress:

Ibrahim bin Muhammad bin Sa`d narrated from his father, from Sa`d that the Messenger of Allah (ﷺ) said:“The supplication of Dhun-Nun (Prophet Yunus) when he supplicated, while in the belly of the whale was: ‘There is none worthy of worship except You, Glory to You, Indeed, I have been of the transgressors. (Lā ilāha illā anta subḥānaka innī kuntu minaẓ-ẓālimīn)’ So indeed, no Muslim man supplicates with it for anything, ever, except Allah responds to him.”

The Qur’an itself hints at this: after describing how Jonah was saved, it adds that this is how God saves the believers (Qur’an 21:88). So Muslims recite this short prayer in illness, debt, grief and fear — trusting that the God who heard a man inside a fish will hear them too.

Honouring Jonah

Because Jonah’s story includes a mistake, someone might be tempted to look down on him. The Prophet Muhammad ﷺ firmly closed that door:

Narrated Abu Huraira: The Prophet (ﷺ) said, "None should say that I am better than Yunus bin Matta

The Qur’an also says that God chose Jonah and made him one of the righteous (Qur’an 68:50). Muslims honour him as a noble prophet whose story shows the power of repentance, not as a failure.

What Jonah teaches

Jonah’s story teaches that no darkness is too deep for God to reach, that the way out begins with honesty about ourselves, and that patience with people is part of calling them to good. It also teaches that God’s mercy is wider than our expectations — for a prophet in the sea and for a whole city on the shore. To read more about turning back to God, see Repentance and Forgiveness, or meet the other prophets in The Prophets in Islam.