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Controlling Diseases of Lilies

by Gary Platford


Gary Platford was co-chair of The Prairie Garden Editorial Committee. He has retired from Manitoba Agriculture and Food, where he was the provincial plant pathologist

Lilies are susceptible to a number of serious diseases caused by fungi and viruses. There are also physiological disorders that affect lilies which are caused by unfavourable growing conditions or environmental stresses. The first step in successful disease control is to prevent the problem from getting started. This can be accomplished by using disease free commercial planting stock. Planting "gift" bulbs from a fellow gardener is often a sure way of introducing diseases into the garden. If a problem does develop, it is essential that the cause of the disease or disorder be established. This can be accomplished by referring to publications such as the "Lily Disease Handbook," a publication of the North American Lily Society. Samples can also be submitted to a provincial or state plant disease diagnostic laboratory or clinic.

Some of the more important types of diseases are listed here:


The two most serious diseases of lilies caused by fungi are basal rot and botrytis blight. Basal rot is caused by one or a combination of several soil borne fungi including species of FusariumCylindrocarpon and Pythium. All of these fungi are soil borne. Infection takes place through the roots and base of the scales. Affected bulbs exhibit a chocolate brown rot and may eventually completely decay from the disease. Indications of a basal rot problem are chlorosis or yellowing of leaves, stunting and premature death of plants.


  1. Plant only disease free bulbs when available from suppliers.
  2. Discard any planting stock showing pockets of rot, or if the plant is only lightly infected, separate the bulb and use clean healthy scales or stem bulblets. 
  3. Rogue out infected plants and replace soil around the plant to a depth of 45cm (18in). 
  4. Avoid over fertilization, especially the use of fertilizers high in nitrogen. 
  5. Mulching around plants will help to reduce soil temperatures. High soil temperatures are particularly favourable for development of basal rot caused by Fusarium
  6. Improve soil drainage as basal rot is favoured by excessively moist soil conditions. 
  7. Avoid mechanical damage to bulbs and prevent injury by soil insects and nematodes, as infection occurs more readily through wounds. 
  8. Treat bulbs prior to planting with bulb dust or a liquid soak treatment containing Benomyl. 
  9. In severe cases where the soil is thoroughly contaminated it may be necessary to resort to the use of a soil fumigant such as Vapam. Treatment should be done in the early fall and planting of bulbs the following spring. Bulbs should not be planted into fumigated soil until all evidence of the fumigant has disappeared. The soil can be tested for presence of fumigant by planting a quick germinating seed such as radish. If the radishes fail to germinate or die very soon after germinating then the soil should be allowed to air out for a further period of time and be retested.


Botrytis Blight

Botrytis blight causes a yellow to orange or reddish brown leaf spot. Under damp conditions spots may become covered with greyish mould growth. Spots soon dry out and the affected leaf area becomes thin and brittle and appears translucent. Heavily infected leaves are often killed by the botrytis blight. Infection typically starts at the bottom of the plant and progresses upward. Flower infection can also occur during periods of cool moist weather. Affected flowers exhibit a wet slime rot and presence of grey botrytis spores are often evident.


Destroy all tops of old plants in the fall. Spray with Benomyl or Chlorothalonil fungicides beginning at the first evidence of leaf spots. Spraying should be done only when the foliage is dry. Complete plant coverage including the underside of leaves is essential for good control. Some lily varieties are listed as being resistant to Botrytis.

Other Fungus Diseases

 There are several other fungus diseases which occasionally occur. These include bulb rots due to sclerotium, bulb rot, black scale disease and blue mould. To control these diseases discard infected bulbs and plant only healthy bulbs. In addition to bulb rots lilies can be affected by root rots caused by soil borne fungi. Root rots can be controlled by improving cultural practices, especially soil drainage and avoiding overwatering. Apply a soil drench of fenaminosulf (Lesan), or etridiazole (Truban). Soil fumigation as for bulb rot, with Vapam, will also eradicate soil borne fungi that cause root rot.

 Damping off can be a problem when growing lily seedlings. Control by using only pasteurized soil or soiless mix. Seedlings should be planted into clean sterilized pots or flats. Used pots and containers should be washed to remove all soil particles and then dipped in a 10% bleach (sodium hypochlorite) solution. Provide good growing conditions, i.e., a well drained soil mix, good air circulation and moderate, not excessive, humidity. Provide adequate light levels for good seedling growth. If necessary, as evident by presence of wilted seedlings, apply a fungicide soil drench of oxine benzoate (Nodamp) or etridiazole (Turban).

 In addition to infections and diseases caused by virus and fungi, lilies may be affected by physiological or environmental disorders. Yellowing of plants may be caused by inadequate fertility, poor soil aeration and drainage and/or a highly alkaline soil reaction. Poor growing conditions often predispose plants to diseases caused by fungi. Successful disease control depends on planting of healthy disease free stock, rouging out and discarding infected plants, timely insecticide sprays to control leaf light and provision of ideal growing conditions. If a disease problem occurs and the cause is not evident from past experience or reference publications, then obtain a diagnosis from a plant disease clinic and follow recommended control measures.


There are three important diseases caused by viruses that infect lilies and cause weakening or degeneration of lily plants. Symptoms include leaf mottling or flecking. Leaves may show alternate areas of light green and darker green colouration. Some viruses cause a rosetting or stunting of plants. Flower production can be affected by virus diseases. Fewer and smaller flowers may be produced. Flower breaking, that is, streaks of white or green colouration in normally coloured flowers, is a fairly distinct symptom of a virus infection. Confirmation of the precise virus affecting a plant requires special diagnostic techniques that are not routinely available at most provincial and state plant disease clinics. These tests can be done by some research laboratories if the problem is sufficient to warrant the test. In any case, bulbs affected by virus diseases cannot be treated to eradicate the virus and should be destroyed to prevent spread of the virus disease.

 Plant new virus free bulbs in an area isolated from known virus infected lilies. All of the virus diseases affecting lilies are spread by aphids. Controlling aphids by recommended insecticide sprays will aid in the prevention or spread of virus diseases. There are some varieties of lilies that are highly tolerant of virus. Variety descriptions in the suppliers’ catalogue should be checked to see if virus tolerant varieties are available. Lily virus diseases are not seed transmitted so virus free material can be obtained from seed of virus infected plants.


Reprinted with permission of The Prairie Garden Committee, Winnipeg Horticultural Society