John Thomas, a first cousin of Gruffydd Thomas, inherited the Thomas estates in 1676. He lived chiefly at Pen-y-bryn, Aber, served as sheriff of Caernarfonshire, and remained lord of Aber at least from 1686 until his death.

The source distinguishes his confirmed lordship from Lord Bulkeley's apparent temporary possession around 1680.

Research sources:
- Dictionary of Welsh Biography, 'Thomas family, of Coed Helen (or Alun) and Aber, Caernarfonshire,' citing PRO C7/339/71, U.C.N.W. Garthewin MS 2077, U.C.N.W. Baron Hill MS 3133, and Caernarfonshire record office material. — https://biography.wales/article/s-THOM-COE-1500.html