A severe lung condition, possibly asthma, caused him to move to South Africa and take up the post of principal at the newly established Shaw College in Grahamstown.

He entered into a fruitful exchange of specimens and correspondence with Asa Gray of the States, Sir William Hooker of Kew and with Harvey and Sonder who were working on the Flora Capensis.

Finding it a drain on his own time to supply duplicates to overseas collectors, he formed the South African Botanical Exchange Society, which brought together a large number of amateur botanists.

Eventually he became head of natural sciences at Gill College, Somerset East, South Africa and then later director of the Cape Town Botanical Garden.

Plant pathology as a science in South Africa formally began in 1887 with the appointment of Peter MacOwan as the consultant in economic botany to the Cape Government.