The manuscripts of R. H. Thomas contain :
- A genealogical table of the family of Cae'r Ffynnon, Pentraeth.
- A commonplace book.
- Essays on various subjects such as Goronwy Owen, nonconformity in Anglesey, the history of Penygarnedd Chapel, Anglesey, notes on William Lewis of Glasinfryn and the C. M. cause in Cefniwrch.
- Details of sermons preached at Penygarnedd Chapel, 1911-1933, together with minutes of monthly meetings etc.
- Poetry written by R. H. Thomas.
- Letters addressed to R. H. Thomas.
- A collection of Anglesey folklore entered for an Eisteddfod competition in 1908.
- An autobiography by Lewis Owen, husbandman.
- Two account books of Hugh Thomas, tailor, 1866-1888.
- Two notebooks belonging to Hugh Williams of Minffordd, Llansadwrn containing accounts, notes and poetry, 1857-1858.
- Vestry book of Llanfair Mathafarn Eithaf, Anglesey, 1821.
- Volume containing the accounts of the Overseers of the Poor in Aston, near Birmingham, co. Warwick along with acts and orders etc. of the governors of the Aston Workhouse, 1700-1730. Also miscellaneous notes relating to Aston and Birmingham. The volume contains manuscript notes made at a later date by R. H. Thomas, such as copies of church registers, compiled for genealogical purposes.
- Notes on sermons by Thomas Smith of Llangeinwen, 1820's - 1830's.
- An essay on the old characters from the Penygarnedd and Rhoscefnhir areas, entered for Eisteddfod competition in 1928.
- Accounts of Glasinfryn Chapel, Llanbedr-goch, Anglesey, 1898.
- Accounts of Salem Chapel, Mynydd Bodafon, Anglesey, 1840-1849.
- Accounts of Pentraeth Chapel, 1869-1877.
- Notebook of the appointments of Rev. Richard Owen, Penygarnedd, 1844-1858.
- Poetry of Gwilym Gwalia.