Mint rust is an infection of the rust fungus Puccinia menthae and causes dusty spots on leaves as well as pustules and often resulting in plant death or severe stunting. Mint rust affects a number of mint species, but related species like marjoram can also be susceptible. Chemical controls are not available for use on mint that is intended for eating so getting rid of mint rust in the home herb garden requires non-chemical options.
Remove infected plants as early as possible. The first cycle of the mint rust fungus creates stunted, pale shoots on mint in spring. If at all possible, remove these shoots and destroy them before they develop clusters of pustules, which release infectious spores. If the rust problem is noticed later, remove the infected plants before the rust spots have turned black, as these black spots release spores that overwinter in the rhizomes of the mint and surrounding soil.
Transplant healthy plants to a new garden bed, but monitor them carefully for signs of rust infection. If rust spots appear, discard all plants and begin a new mint patch with fresh mint plants or new seed.
Prevent mint rust spore that may be present in the rhizomes of plants from surviving winter by washing the rhizomes in water that is 111 degrees Fahrenheit in autumn.
Leave in the hot water for 10 minutes then cool them in cold water and replant. Do not exceed 111 degrees Fahrenheit, as this will kill the plant.