Cryopreservation is one of the ideal and suitable methods for long-term storage of plant germplasm. The plant contaminated with diseases and pathogens are decreased the multiplication rate, survival rate and high quality of plants after cryopreservation. The aim of this work was to improve a micropropagation method for lily in Korea, which is indigenous plant. In the last process of rinsing scales after surface-sterilization, we tried to control the diseases and pathogens lived within the tissue by rinsing in 0.03% sodium hypochlorite (NaClO) instead of sterile distilled water. Bulb scales of Lilium were cultured in vitro on MS medium supplemented with Plant Preservative Mixture (PPM). The results showed that L. tsingtauense accessions were observed ranged from 53.9 to 100% with a mean value of 76.8% and L. hansonii accessions were checked from 84.5 to 85.5% with a mean of 85% survival rate. The newly small bulb formed from bulb-scales was transferred to MS medium. We checked the presence of microorganisms and survival rate after 3 weeks in culture after examination of bacterial incidences. The results indicated that the non-contamination rate were shown ranged from 75.0 to 94.1% with mean value of 83.2% in L. tsingtauense species, and that L. hansonii were observed 85.1 to 91.7% with mean value of 88.4%. This study will provide a valuable basis for establishment of effective axenic cultures for in vitro micropropagation of Korean native lily species.