1880 census of Apache Co., Arizona territory, Sunset precinct, enumerated 2 June, lists on p. 6 as family #51/52:
Johnston, Wm Jas, 57, b. U.S. U.S. U.S., shepherd; Ellen, wife, 30, b. England England England; Margaret E., dau, 14, b. Utah U.S. England; Samuel, son, 12, b. ditto, shepherd; Elizabeth, dau, 10, b. ditto; Clara, dau, 2, b. Arizona U.S. England.

1900 census of Valencia Co., New Mexico territory, Wingate precinct, enumerated 7 June, lists on p. 4A as family #54:
Johnston, William J., 75, b. Aug 1824, Ohio Ohio Ohio, farmer; Allan J., wife, 55, b. July 1844, England England England, married 32 years, mother of 9 children, 6 living; Margaret, dau, 34, b. July 1865, Nevada married 0 years, mother of 0 children, Nevada Ohio England; Samuel, son, 32, b. Aug 1867, Utah Ohio England, married 1 year; Elizabeth, dau, 30, b. Oct 1869, married 1 year, mother of 0 children; George, son, 19, b. Feb 1881, Arizona Ohio England; Rebeccca, dau, 16, b. June 1883, NM Ohio England; Jessie, son, 12, b. Sep 1886, NM Ohio England.

Margaret is also listed in Fruitland, San Juan Co., New Mexico with her husband James Barton Ashcroft, but I cannot find another listing for Elizabeth, nor can I find her children in 1900. They had really been married respectively 18 and 14 years, with several children each. It is unclear whether the three older married children were visiting their parents, or whether William and Ellen misunderstood the census instructions and reported all their living children, whether in the household or not.