And some of the people of Judah, Benjamin, Ephraim, and Manasseh lived in Jerusalem:
The first verse looks back upon the foregoing genealogies, and tells us they were gathered out of the books of the kings of Israel and Judah, not that which we have in the canon of scripture, but another civil record, which was authentic, as the king's books with us. Mentioning Israel and Judah, the historian takes notice of their being carried away to Babylon for their transgression.
Commenting on 1 Chronicles 9:1-13
And in Jerusalem dwelt of the children of Judah, and of the children of Benjamin,.... Of which tribes were the largest number that went into, and returned out of, captivity: and of the children of Ephraim and Manasseh; such of those tribes who had joined the others when Jeroboam introduced his idolatry, or had fled to them when Samaria was besieged and taken by Shalmaneser...
And in Jerusalem dwelt - Several of the tribes of Judah, Benjamin, Ephraim, and Manasseh, took advantage of the proclamation of Cyrus to return to Jerusalem, and so mingled with the Israelites, and those to whom Jerusalem had previously appertained; and this was necessary in order to provide a sufficient population for so large a city.