Jasmonic acid (JA), an essential plant hormone controlling the plant defense signaling system and developmental processes, has stereospecific bioactivities that have not been well understood mainly due to the limitation in separation and detection methodologies. In this work, a fast CE-UV method based on short-end injection technique and a sensitive CE-QTOF-MS method based on partial filling technique were successfully developed for the enantioseparation of racemic JA. The successive coating technique was also involved by modifying the capillary with multiple ionic polymer layers of polybrene-dextran sulfate-polybrene. This was the first report on the direct resolution of both pairs of JA enantiomers, including two naturally occurring JA stereoisomers. Although no pure JA stereoisomers were commercially available, all the separated JA stereoisomers were identified indirectly by comparing the difference between the racemic standard and plant samples based on the presence and the ratio of each stereoisomer. Satisfactory results were obtained in terms of sensitivity (LOD, 24 ng/mL or 0.7 fmol for single JA stereoisomer) using 45 mmol/L ammonium acetate at pH 4.5 containing 70 mmol/L alpha-CD as the buffer system. This established CE-QTOF-MS method was later successfully applied for the study of the naturally occurring JA stereoisomers in wounded tobacco leaves.