The n-butanolic fraction of a methanolic extract (80%) from aerial parts of Ajuga chamaecistus ssp. tomentella was analysed using different chromatographic methods. Column (CC) and high-performance liquid chromatography (HPLC) were used for isolation and purification. 13C, H NMR, H-H COSY, HSQC, HMBC, and ESI-MS were employed for identification of the compounds isolated from this fraction. The structures of the compounds were determined to be cis-melilotoside (1), trans-melilotoside (2), lavandulifolioside (3), 20-hydroxyecdysone (4), leonoside B (5), martynoside (6), ajugalactone (7), makisterone A (8), and 24-dehydroprecyasterone (9). This is the first report on the presence of cis- and trans-melilotoside in Ajuga species. Cytotoxic evaluation of the n-butanolic fraction, cis- and trans-melilotoside against cancer (T47D, HT-29, and Caco-2) and normal (NIH 3T3) cell lines by the mitochondrial tetrazolium test (MTT) showed no cytotoxic effects up to 400 microg/mL. The results of this study suggest that melilotoside, phenylethyl glycosides, and phytoecdysteroids are the main constituents of the n-butanolic fraction of Ajuga chamaecistus ssp. tomentella.