To generate transgenic lily plants with no selectable marker and improved tolerance to abiotic stress, two vectors were co-transformed into the Lilium oriental hybrid Sorbonne by particle bombardment. The pKSB vector included the Cre/loxp-mediated site-specific cDNA excision system under control of the inducible promoter rd29A, and the pBPC-P5CS-F129A vector carried the P5CS gene, which we hypothesized would improve resistance to drought and salt stresses in transgenic lily plantlets. The presence of the two genes was simultaneously detected by PCR and Southern blotting in two resistant plantlets. The co-transformation rate was 0.16%. Subsequently, inducer expression was tested under varying conditions to optimize the deletion of marker gene. Results from molecular detection assays revealed that maintaining bases of bulblet scales at 4 degrees C for 12 h resulted in an increase in the excision rate, reaching 60%. Expression of P5CS improved resistance to salt stress in transgenic lily plantlets. These results demonstrated the feasibility of using the Cre/loxP-based marker elimination system to generate marker-free transgenic plantlets with improved stress tolerance.