When the kingdom of Israel split from the kingdom of Judah, the two nations acted as allies (1 Kings 22). As time went on, they began to mistrust each other and actually began to fight against one another. This was abominable to the Lord because they were all brethren and should have been at peace with each other. For an example of the conflict between these two nations, see the commentary for 2 Nephi 19. Isaiah is prophesying that all enmity between these two will be gone in the last days.
LeGrand Richards
"We are from Ephraim. The Lord expects us, since we are the custodians of his gospel as restored in these latter days, according to my understanding, to extend the hand of friendship to Judah, because after all we are all descendants of the prophets Abraham, Isaac, and Jacob, and we come under the promises that through their descendants should all the nations of the earth be blessed.
"I do not know how the enmity and the envy between Ephraim and Judah can disappear except that we of the house of Ephraim, who have the custody of the gospel, should lead out in trying to bring to this branch of the house of Israel the blessings of the restored gospel…
“And it seems to me that the only way that the tribe of Judah can be sanctified to dwell in his presence forever and ever will be when we bring to them the gospel of the Lord Jesus Christ as the Savior promised them it would be brought in the latter days.” (Conference Report, Oct. 1956, pp. 23-24 as taken from the 1981 Old Testament Institute Manual, p. 150)