Colchicum species, which have been widely used as a medication for years, still remain important in treatment of Familial Mediterranean Fever, gout and Behcet's Disease. In the present work, alkaloids, phenolic compounds and cytotoxic activities from different parts of two Colchicum species, namely C. chalcedonicum and C. micranthum were investigated for the first time. From different parts of two species, alkaloids were isolated and colchicine concentrations were also determined by HPLC. The methanol extracts were investigated for their cytotoxic activity against the A549 cell line using the MTT and LDH methods. Additionally, the phenolic compounds of each extract were investigated by LC MS/MS. Six alkaloids, namely colchicine, colchifoline, 2-demethylcolchicine, demecolcine, 4-hydroxycolchicine and N-deacetyl-N-formylcolchicine were isolated from different parts of two species. The autumn corm of C. micranthum possessed the highest amount of colchicine among all extracts. All extracts showed high cytotoxicity, while the highest toxicity was determined in the seed extract. According to the LC MS/MS analysis, 19 phenolic compounds were shown to be present. This is the first study which highlights that the seeds of C. chalcedonicum and autumn corms of C. micranthum could be valuable for the pharmaceutical industry to obtain colchicine and other tropolone alkaloids.