Green wild plants (dirctly before flowering) and seeds of Hyoscyamus aureus were collected from natural habitat at Al Qalamon region in Syria. Seeds were surface sterilized and cultured in vitro, after 21 days from germination stem-derived callus was induced on two different nutrient media. Tropane alkaloids were extracted from wild plants and 30 days old in vitro plants and callus, and then analyzed using GC-MS. Genetic variation was also studied between the wild and in vitro plants and the callus culture lines using twenty ISSR markers. The results showed that there were significant variations in tropane alkaloids contents between the wild plants, the in vitro plants and the callus culture lines. The highest content of hyoscyamine was in callus on line A medium, but the highest content of scopolamine was in the wild plants. However, the lowest content of tropane alkaloids was in callus on line B medium. Also the ISSR analyses showed that there was genetic variation between the wild and in vitro plants and the callus culture lines.