בס"ד
The commonly held belief in most Jewish and Christian circles is that the Samaritans are the descendants of peoples sent into Israel to replace the exiled northern tribes of Israel.
Indeed, such people were planted in the land as can be seen in the biblical narrative from 2 Kings, Chapter 17
24 And the king of Assyria brought men from Babylon, and from Cuthah, and from Avva, and from Hamath and Sepharvaim, and placed them in the cities of Samaria instead of the children of Israel; and they possessed Samaria, and dwelt in the cities thereof.
25 And so it was, at the beginning of their dwelling there, that they feared not the L-rd; therefore the L-rd sent lions among them, which killed some of them.
26 Wherefore they spoke to the king of Assyria, saying: 'The nations which thou hast carried away, and placed in the cities of Samaria, know not the manner of the G-d of the land; therefore He hath sent lions among them, and, behold, they slay them, because they know not the manner of the G-d of the land.'
27 Then the king of Assyria commanded, saying: 'Carry thither one of the priests whom ye brought from thence; and let them go and dwell there, and let him teach them the manner of the G-d of the land.'
28 So one of the priests whom they had carried away from Samaria came and dwelt in Beth-el, and taught them how they should fear the L-rd.
29 Howbeit every nation made gods of their own, and put them in the houses of the high places which the Samaritans had made, every nation in their cities wherein they dwelt.
Misidentification
The Biblical narrative never identifies these imported pretenders as Samaritans. To the contrary, the narrative explicitly states that Samaritan/Samarian Israelite culture pre-existed the import of the foreigners. Verse 28 tells us that it was a Kohen of Samaria that was brought from Beth-El to teach the foreigners how to fear G-d. Verse 29 further informs us that the foreigners set up their own national gods in the houses of the high places that the Samaritans had built. A clear distinction is made between the previous, Samarian (Shomroni) Israelites and the foreigners who were brought in to supplant them.
It is likely that the Assyrians only exiled the aristocracy, leaving the peasants behind, just as the Babylonians did with the Judeans in 586 BCE. And in fact, Assyrian historical chronicles seem to indicate that not all the Israelites were exiled. Instead of stating that all inhabitants were taken captive, we are given an exact figure. The annals of Sargon II, king of Assyria state quite clearly:
"I besieged the city of Samaria....I led away 27,290 of its inhabitants as captives and took some of them as soldiers in my regiments. I rebuilt the city and settled it with peoples from the lands of my conquests."
The peasants were probably left behind because they were less likely to plot rebellion. In fact, our Bible bears witness to this Israelite remnant still existing as a distinct community even in the late first temple period, long after the destruction of the northern kingdom.
II Chronicles 34 Describes repair work done on the Temple and a collection that was taken to finance it. In verse 9 we read: "They went to Hilkiah the high priest and gave him the money that had been brought into the temple of G-d, which the Levites who were the doorkeepers had collected from the people of Manasseh, Ephraim and the entire remnant of Israel..."
And this distinct Samarian culture is attested to even after the destruction of the 1st temple. In Jeremiah 41, when Gedaliah ben Ahikam is assassinated, we are told that
"The day after Gedaliah’s assassination, before anyone knew about it, eighty men who had shaved off their beards, torn their clothes and cut themselves came from Shechem, Shiloh and Samaria, bringing grain offerings and incense with them to the house of the L-rd."
Obviously these men were still worshipping at the Temple in Jerusalem, yet mingled pagan customs into their worship.
This remnant of Israel were most likely taking wives from among the Cuthim and other foreigners that were sent to the area. The Northern tribes had a very different culture than the Judeans and had no problems whatsoever marrying foreign women. This intermarriage is most likely what gave rise to the epithet Cuthi.
That would account for some interesting Samaritan genetic qualities. In 2004, an article was compiled by numerous genetic researchers from many of the world's top universities. See Reconstruction of Patrilineages and Matrilineages of Samaritans and Other Israeli Populations From Y-Chromosome and Mitochondrial DNA Sequence Variation. Their research found that the Samaritans paternal genetic makeup is quite similar to that of other Jewish communities, but having maternal genetic features like those of the surrounding population. They also note that the genetic makeup of the Samaritan Kohanim indicates that they are from a very scrupulously guarded line of kohanim that married non-Jewish wives, as evidenced by the makeup of their mitochondrial DNA. The Samaritans have traditionally had an above average number of Kohanim among them.
Where did all those Kohanim come from? Our biblical evidence would seem to support that the Samaritans are indeed the descendants of Israelites that escaped the Assyrian exile, but it doesn't explain this line of pure, paternally descended Kohanim that also have non-Jewish women as their progenitors. The answer to the presence of this peculiar priestly line among the Samaritans seems to be supplied by Josephus.
Josephus Antiquities, Book 11:8:2 (4th-5th BCE) But the elders of Jerusalem being very uneasy that the brother of Jaddua the high priest, though married to a foreigner, should be a partner with him in the high priesthood, quarreled with him; for they esteemed this man’s marriage a transgressing about the marriage of [strange] wives, and that this would be the beginning of a mutual society with foreigners, although the offense of some about having married wives that were not of their own nation, had been a result of their former captivity, and of the miseries they then underwent; so they commanded Manasseh to divorce his wife, or not to approach the altar, the high priest himself joining with the people in their indignation against his brother, and driving him away from the altar. Whereupon Manasseh came to his father-in-law, Sanballat, and told him, that although he loved his daughter Nicaso, he was not willing to be deprived of his priesthood on her account. And then Sanballat promised him not only to preserve to him the honor of his priesthood, but to procure for him the power and dignity of a high priest, and would make him governor of all the places he himself now ruled, if he would keep his daughter for his wife. He also told him that he would build him a temple like that at Jerusalem, upon Mount Gerizim, which is the highest of all the mountains that are in Samaria; and he promised that he would do this with the approbation of Darius the king. But there was now a great disturbance among the people of Jerusalem, because many of the priests and Levites were entangled in such matches; for they all revolted to Manasseh, and Sanballat afforded them money, and divided among them land for tillage, and habitations also, and all this in order every way to gratify his son-in-law.
The Key to Understanding It would seem that Josephus has just given us the missing piece to the Samaritan puzzle. From the Biblical, historical and genetic evidence cited above, it seems most probable that the Samaritans are the descendants of the remnant of Efraim, Menasheh and the other tribes, renegade priests from Jerusalem and all those Judeans who refused to accept the reforms of Ezra.
It appears that this is where and when the real schism with normative Judaism took place. The Samaritan claim is that the great rift took place in the time of the judges, with Eli the priest breaking away and setting up a rival tabernacle and altar at Shiloh. However, a schism during the time of Ezra is more likely and is oddly enough evidenced in the writings of the Samaritans themselves. The Jewish Encyclopedia article on the Samaritans has an interesting tidbit in its description of the Samaritan Messiah doctrine. The last line of this quote leaves no doubt as to who the real antagonist was in the eyes of ancient Samaritan theologians.
The 'Taheb' - The Jewish Encyclopedia
The Messiah doctrine, which, though of less importance, is clearly defined. The term used is 'Taheb', which has been variously explained as "the restorer" or "he who returns." During all the time that has elapsed since the schism of Eli and the disappearance of the Tabernacle, the world (i.e., Israel) has been suffering under the divine displeasure. This is called the period of 'Panutha'. It will be terminated by the coming of the Taheb, who will restore the period of favor, establish the true religion, and destroy the followers of Ezra."
The answer can be more confusing than the question
I began this article by asking "Who are the Samaritans?" All evidence seems to suggest that no matter what their beliefs and behavior past and present, the fact is that Biblically, historically and genetically, the Samaritans are descendants of Aharon, Ephraim, Menashe and the rest of the remnant of Israel.
This answer settles very little. In fact, it only serves to raise a much more complex question. Now that we know who they are, how should we as Jews, relate to them?