In many other variants recorded during the colonial era, Thomas of Cana had two wives or partners, one of them being the ancestor of the endogamous Southists, and the other one being the ancestor of the Northist.[13][22] These variants are considered apocryphal and are not the accepted tradition among contemporary Northist and Southist scholars who generally believe them to be the consequence of rivalry between the St. Thomas Christians and Knanaya.[12] In some of these variants, the Southists' ancestor was Thomas’ Syrian wife, while the Northists' was an indigenous Nair woman who became his second wife or concubine, implying that the Southists are Thomas’ true heirs.[29] In other variants, both wives were Kerala natives, while the Southists' forebearer was from a higher caste.[30] More recent versions of this story downplay the importance of either wife's status, focusing instead on their descendants' marriage practices: the Northists intermarried with the natives, while the Knanaya enforced strict endogamy, maintaining a "pure" lineage.[31]

Some Northists also maintain versions of the Thomas of Cana story that counter the Knanayas' assertions. In the Northist versions, both Northists and Southists are descended from marriages between Thoma's party and indigenous Christians, but the Knanaya are descended from Syrian servants who married "low caste" Keralans; the Knanayas' endogamy and "purity" are thus borne out of their exclusion by the higher class Northists. These variants frequently trace Knanaya descent back to a dobi (washerwoman); in some versions of this story, she became Thoma's concubine, while in other she married a lower-caste Maaran boy.[32] This assertion is based on the 1676 Portuguese document "M.S Sloane 2748-A", a likely forgery attributed to the Carmelite priest Father Mathew.[33]

Historian of medieval India and Northist priest Pius Malekandathil argues that the two-wives legend was simply a creation of rivalry between the Middle Eastern migrant Knanaya and the Native St. Thomas Christians. Malekandathil expresses that the story originated in the medieval era due to the two ethnic groups of Christians asserting socioeconomic dominance over the other. Furthermore, Malekandathil notes that the two-wives legend is not the accepted tradition among the people of Kerala but instead that the indigenous Saint Thomas Christians got the appellation "Northists" because they were initially located on the northern part of the city of Cranganore, while the migrant Knanaya under the leadership of Thomas of Cana were given the southern side of the city which led to the generic title of "Southists".[12]

Another story regarding the origin of the division became popular during the 20th century. In 1939, Knanaya politician and author Joseph Chazhikaden published a book on the community, Tekkumbhagasamudayam Charitram, in which he argued that the Knanaya were the descendants of ancient Jews. Chazhikaden built upon the Thomas of Cana tradition but asserted that Thomas' followers originated in Judea. According to Chazhikaden, the group converted to Christianity while maintaining their distinct culture and identity.[31] Eventually, they were forced out of their homeland and moved to Cranganore, where they were welcomed by the ruler Cheraman Perumal and lived near, but maintained their separateness from, the indigenous "Northist" Saint Thomas Christians. Swiderski believes that the legend was "conceived and promulgated" by Chazhikaden himself.[34] Many modern Knanaya accept the account as factual, while others reject it. As with other Knanaya origin traditions, some Northists dispute and condemn it