Jonathan Crowther married Cecilia Johanna Petronella Delport (Oudtshoorn, Western Cape, 20 July 1856 – Vegkop, Heilbron, Orange Free State, 1 August 1941) and had a daughter and a son by her.

After the outbreak of the Second Boer War in October 1899 Crowther became the commander of the Ladybrand and Ficksburg commandos and later fighting general (Afrikaans: veggeneraal).

[4] Crowther retreated to positions in the Brandwater Basin guarding the passes of the Drakensberg escarpment, under the higher command of Marthinus Prinsloo.

De Wet left the Basin on the night of 15 July 1900 with 2000 men and president Steyn and the other members of the Orange Free State government.

Crowther left Ceylon for South Africa on August 7, 1902, with 26 other released Boer officers in a second batch of 400 prisoners of war.