On 20 June 1832, John married Martha Bowen at All Saints Church, Mochdre. Martha was a farmer's daughter - born in 1813 in Mochdre, baptised at All Saints on 8 May 1813. Her parents were Thomas Bowen and Jane Turner.
The couple lived in Mochdre for most of their married lives, farming first at Hendre Farm and then at The Hafod. They had several children:
Martha Jones 1832-1886
Mary Ann Jones 1834-1917
Jane Jones 1836-??
Elizabeth Jones 1838-??
John Jones 1841-??
Ann Catherine Jones 1846-1934
Sarah Lavinia Jones 1853-??
By 1871 John had retired from farming and was living in the Hendidly suburb of Newtown, Montgomeryshire, with Martha and their youngest daughter, Sarah.
Martha died on 16 November 1879 of chronic bronchitis, in Welshpool, Montgomeryshire. She was probably staying with daughter Sarah and her husband John Morgan. John moved to live with daughter Elizabeth and her husband Thomas Morris in Llandinam, Montgomeryshire, and was there for the census in 1881. Shortly after the census, in July 1881, John died.