Kalanchoe (Kalanchoe blossfeldiana) is a common potted flower that is popular throughout the world. Brown spot (caused by Stemphylium lycopersici) is one of the common foliage diseases in kalanchoe. This disease tends to infect leaves of kalanchoe plants in hot and humid environments, reducing their aesthetic value. The current investigation aimed to generate mutations resistant to brown spot in ‘Mary’ kalanchoe through chemical mutagenesis followed by molecular marker identification. Putative mutants were developed by treating embryogenic calluses with ethyl methanesulfonate (EMS) at median lethal doses (LD50)–either a 0.8% concentration for 2 hours or a 1.0% concentration for 0.5 hours. Brown spot crude toxin solution was used as the selection agent to identify disease-resistant calluses during tissue culture. The optimal crude concentration (60%) was determined by soaking calluses with different concentrations of crude pathogen: 0%, 20%, 40%, 60%, and 80% (v/v). A total of 32 anti-brown spot lines were regenerated and tested for disease resistance with detached leaves. Three regenerated EMS mutant lines showed no obvious brown spot lesions on their leaves after the disease resistance assay and were subjected to polymorphism identification by start codon targeted (SCoT) molecular markers. Three (SCoT40, SCoT71, and SCoT72) of 45 selected primers were chosen to identify the mutants. This work may lay the foundation for further development of new disease-resistant cultivars of kalanchoe.