Lilium ledebourii is a rare Asian species and is an endemic plant of Iran which grows in Gilan province in Damash highlands. In this study, the structural features of flower including the study of sections such as carpel, stamen, and tepals were performed. This plant had a full flower that consisted of six tepals (three petals and three petal-like sepals ), six free stamens and a 3-lobed gynoecium. In the cross-section of tepals, the stomata as well as cells containing anthocyanins were observed. In stamens, anther (epidermis, endothecium, middle layers and an innermost tapetum ), and filament were observed. In the gynoecium, ovary (ovary wall, locule, funiculus, anatropous ovule, different arrangements of vascular bundles, transmitting tissue and stomata ), style (stylar canal and transmitting tissue ), and dry stigma with elongated papillae tissue were observed. Besides, the presence of alkaloids in the bulb was tested using Wagner and Dragendorff reagents and the total alkaloid content in three types of methanol, ethanol, and butanol extraction was investigated. The ethanol extract had a significant difference with other extractions. The methanol extract was chosen for further investigation by gas chromatography-mass spectrometry (GC-MS )and two compounds of Pterin-6-carboxylic acid, and Pyrrolizin-1, 7-dione-6-carboxylic acid, methyl (ester) were detected.