This short dua encompasses the concept of tawheed, one of the most basic tenets of Islam. By saying this dua, you are consciously and deliberately declaring that Allah (swt) is the only deity, the exalted. You then show your humility by admitting your faults and weakness.
Arabic : لَّآ إِلَٰهَ إِلَّآ أَنتَ سُبْحَٰنَكَ إِنِّى كُنتُ مِنَ ٱلظَّٰلِمِينَ
Transliteration: la ilaha illa illa anta subhanaka inni kuntu minaz-zalimin
English Meaning: There is no deity except You; exalted are You. Indeed, I have been of the wrongdoers.
This ayat (commonly referred to as Ayat E Kareema or just Ayat Karima) is mentioned in Surah Anbiya Verse 87.
The full ayah goes as follows:
“And [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.” it continues on, “So We responded to him and saved him from the distress. And thus do We save the believers.”
Prophet Yunus gave up on his people. Without the permission of Allah, he decided to leave the city of Nineveh in hopes to find a city that would more readily accept him and the message of Islam. This is why the Quran mentions “the man of the fish, when he went off in anger and thought that We would not decree [anything] upon him”.
As punishment he was kicked off and abandoned by his ship members, swallowed by a whale, and left in darkness. At this moment he cried out remembering Allah, praising Allah, admitting his faults in the matter by saying “Indeed, I have been of the wrongdoers.”
Allah seeing the genuine and sincere apology had then relieve him.
The best form of dhikr is to recite Quran with an understanding of its meanings.