Probably the daughter of John CAROTHERS of Ireland. [1606, p.1155] There was a 38 year old man by that name in the 1800 Pennsylvania Septennial census of Lycoming Twp.

As of 20-FEB-2014, there was a Findagrave memorial (# 121719862) [1498, Memorial# 121719862] for a Samuel THOMPSON (1791-1847) whose wife is listed as Margaret Weisel THOMPSON and that their son was a James THOMPSON whose birth year and wife’s name match those already recorded in this genealogy for this Margaret’s son. (UPDATE: as of 01-NOV-2014 the link from that memorial to James THOMPSON has been deleted). Based on an index of the Lycoming Gazette [3604], there was an article published with the paraphrased title "Samuel Thompson: Administrator of George Weisel estate" on 18-NOV-1835, page 3 (unfortunately Ancestry.com only has page 1 of that edition). This seems to be a good indicator that Samuel's wife probably was Margaret WEISEL. But it is still not clear if that James was their son or the son of Margaret Carothers THOMPSON. Then there is the 1840 census of Hepburn Twp., which shows both a Samuel THOMPSON and a Margaret THOMPSON as heads of separate households (on the same census page), with both of them being tallied in the 40-49 age buckets in their respective households. [1751] The memorial gives a death date for Samuel of 1847 and since James THOMPSON Sr. died in 1834, that is consistent with Samuel being alive in 1840 and Margaret Carothers THOMPSON being a widow at the same time. So again this points to the likelihood that Samuel’s wife was Margaret WEISEL, and the other Margaret in 1840 must have been Margaret CAROTHERS. But, the 1830 census also shows Margaret and Samuel as separate heads of household, this time not only on the same census page but adjacent to each other, both apparently in the 30-39 age bucket, but in Margaret’s household is a male in the 40-49 bucket, so why is he not the head?

Although this still leaves the question of parentage for the younger James, the 1850 census shows James and his mother Margaret, age 60, living near Samuel and Isaac THOMPSON (before the brothers moved to Wisconsin) who were sons of James and Margaret (CAROTHERS) THOMPSON. [701], [702] Perhaps both Samuel and James Sr. had a son named James, but so far only one James has been found in that generation (unless the 1850 James is not the same person as the 1860 James (see below).

The 1860 census for Hepburn Twp. [3601] shows the younger James THOMPSON married with 4 children, and next door is a “Mrs. THOMPSON” whose age is given as 64, and so born circa 1796 (a “Margaret WEISSEL” was born 16 Jan 1796 in Bucks County, Pennsylvania [3605], [1498, Memorial# 121719982] - this is the date & place given on Findagrave). So “Mrs. THOMPSON” could be Margaret WEISEL THOMPSON. Margaret CAROTHERS THOMPSON would have been expected to be listed as age 70 in 1860, if she was the one in the 1850 census. Although the enumeration of that household makes it appear that the four persons listed below Mrs. THOMPSON are also named THOMPSON, it turns out that the enumerator’s ditto marks (“) are in error and that the actual surname of those people is EDLER, as confirmed by the 1870 census for Joseph EDLER. [3603] See also Find A Grave Memorial# 42488582 [1498] for Joseph EDLER. As yet I see no family connection between “Mrs. THOMPSON” and the EDLER family.

The 1870 census of Hepburn shows a 75 year old Margaret living with James and Isabella THOMPSON. Again, this Margaret is consistent with Margaret WEISEL. Perhaps James’ proximity to the sons of Margaret Carothers in the 1850 census was indeed just a coincidence, or perhaps it furthers the speculation that Samuel Thompson (the one married to M.Weisel) and James Thompson (the one married to M. Carothers) might have been brothers.
The memorial for Margaret Weisel Thompson (# 121719982) says she died 9-NOV-1877, whereas a Familytreemaker website lists her death date as 09-FEB-1885. The death date of Margaret Carothers THOMPSON remains unknown. Pinning these dates down would help solve this mystery. James’ mother appears to no longer be living with him in 1880 (same page as Source[1036]), so this suggests the 1877 date may be the correct one for Margaret Weisel Thompson.

Hepburn Twp., Lycoming Co., PA
1830 1 Margaret THOMPSON, age 30-39
1840 1 Margaret THOMPSON, age 40-49
1850 1 Margaret THOMPSON, age 60
1860 1 Margaret THOMSON, age 64
1870 1 Margaret THOMPSON, age 75
1880 none

1820 Census only has a Samuel THOMPSON, age 26-44, in Loyalsock Twp., but also there is a Benjamin THOMPSON, age 16-25, a James THOMPSON, age 26-44, an Isaiah THOMPSON, age 45+, and John CAROTHERS, age 45+ (probably Margaret’s father). Meginness [1606, p.1155] tells us that John CAROTHERS died in Loyalsock. Another Samuel THOMPSON, age 26-44, lived in Moreland Twp.
Did not find James THOMPSON in 1830 Lycoming Co.