Most of my daylilies are in pots and this is no exception. This is the method I use it may not work for others. Usually, there’s little you can do to save plants, so prevention is important. Once the first signs of crown rot are noticed, it’s best to simply pull the infected plants and discard them promptly. Bacterial soft rot, also known as crown rot, is caused from damaged roots or crowns and occurs in rhizomes and at the bases of flowers. A plant’s foliage, crown and roots can become infected quickly, causing a daylily to become mushy and produce a foul odor. On this particular daylily, it was (a) a new plant this spring (b) had already lost one fan to crown rot (c) has not been a vigorous grower. If i have some crown rot in a clump i'm not as concerned as i am with new arrivals and as for seedlings with crown rot COMPOST! Crown rot treatment is difficult, especially if it’s not caught early enough, which is often the case. In Daylilies by Christine Moore 11th February 2017 1 Comment. If crown rot is cought soon enough your chances of saving your daylily may be good! One of the most dangerous problems that daylilies can have is the daylily rot. Daylily Crown Rot. This daylily has over a 1/4 of the crown removed. It generally is caused from nematodes, which are microscopic worms living in the soil. I have a daylily right now that is having the same problem (minus the Chlorosis). Daylilies suffer from bacterial crown and root rot during summer and early autumn in Australia, due to the daylily plant being stressed from too many long hot dry summer days over 35 C our daylily plants put it in hard. Most people may not be aware about it, but if left untreated it causes great damage to the entire plant.