Phenolic compounds are the major bioactive constituents of the Chinese herbal drug Tu-Si-Zi, which is prepared from the seeds of Cuscuta chinensis. However, seeds of C. australis also are offered under the name of this drug in the herb market. In order to make a comparison of their chemical constituents, the phenolic compounds of these two Cuscuta species were analyzed by high-performance liquid chromatography/diode-array detection/electrospray ion trap tandem mass spectrometry (HPLC/DAD/ESI-MS(n)). A total of 50 compounds were observed in the methanol extracts, including 23 flavonoids, 20 lignans and 7 quinic acid derivatives. These compounds were separated on a C18 column and identified or tentatively characterized based on UV spectra and MS fragmentation behavior. In contrast to previous reports, the phenolic patterns of these two Cuscuta species were found to be very different. Kaempferol and astragalin were the predominant constituents of C. australis, while hyperoside was the major compound in C. chinensis. Most of the identified compounds, especially the acylated flavonoid glycosides, have not previously been reported from Cuscuta species. In addition, a 30 Da neutral loss observed for flavonols was investigated and could be used to differentiate flavonoid isomers such as kaempferol and luteolin. The ESI-MS fragmentation behavior of furofuran lignans was also investigated, and a characteristic pathway is proposed. The large differences observed between the phenolic constituents of C. chinensis and C. australis strongly encouraged further comparison of the bioactivities of these two species.