From the Ontario Invasive Plant Council:

Do you how to tell Invasive Phragmites from Native Phragmites?

Invasive Phragmites

High density stands, near monoculture stands of living and dead stems (up to 200 per m2).

Generally, dull tan or beige stems with a rough texture. Grows up to 5m or more

Leaves are typically blue-green

Large, dense seed heads

Native Phragmites

Low density stands, with fewer dead stems and oftenmixed with other vegetation.

Stems are generally shorter and thinner, shiny with a reddish-brown colour in the lower internodes and a smooth texture

Leaves are typically yellow-green

Small, sparse seed heads