A reversed phase high-performance liquid chromatographic method was developed for quantifying E-ligustilide (1) and Z-ligustilide (3) in the roots of Angelica sinensis (Oliv.) Diels with confirmation using UV, atmospheric pressure chemical ionisation (APCI) MS and APCI-MS-MS techniques. Based on the UV spectra of compounds 1, E-butylidenephthalide (2), 3 and Z-butylidenephthalide (4), the absorption at 350 nm was chosen as measuring wavelength in which baseline separation of compounds 1 and 3 could be obtained but avoided the interference of compounds 2 and 4. The identity of compounds 1 and 3 in samples were unambiguously determined by the respective quasi-molecular ions ([M+H]+) in APCI-MS. According to the stability data, acetonitrile was chosen for the preparation of standard solutions in order to minimize the isomerization of compound 3. Compounds 1 and 3 were qualitatively and quantitatively analyzed in seven samples of the roots of Angelica sinensis (Oliv.) Diels, Angelica acutiloba Kitagawa, Angelica acutiloba Kitagawa var. sugiyamae Hikino and the rhizome of Ligusticum chuanxiong Hort. Analysis of an extract from a sample root of Angelica gigas Nakai using LC-MS for the first time could not detect the presence of ligustilide in this herb. The overall analytical procedure is rapid and reproducible which is considered suitable for quantitative analysis of large number of samples.