Dr Morgan takes up the role after 13 years as head of the commission’s plant & seed supply business unit.
He gained a PhD in forestry and a BSc in ecological science from Edinburgh University and has published various research reports and bulletins.
On his new role, Dr Morgan said: "It’s an honour to be asked to lead the commission’s plant health service.
"I’m looking forward to working with colleagues, and with partners elsewhere in government and the forestry community, towards securing a healthy, sustainable future for our trees and forests."
Commenting on the new appointment, Forestry Commission director-general Rim Rollinson said: "I’m delighted that John Morgan has accepted this vitally important role.
"Pests and diseases post an increasing threat to Britain’s trees and forests, and John brings to the post just the kind of breadth and depth of knowledge, skills and experience that we need to lead our efforts to tackle it."