Objectives The aim of this study was to elucidate the molecular events of cell cycle progression underlying alterations in cell morphology, as well as the pro-apoptotic and antiproliferative effects of Sonoran propolis (SP) on cancer cells. Methods Cell cycle progression was analysed in human (HeLa) and murine (M12.C3.F3) cancer cell lines treated with SP, its primarily plant source Populus fremontii resins (PFR), and other potential contributing plants [Bursera laxiflora, Ambrosia ambrosioides, and Ambrosia confertiflora (ACR)]. In addition, bio-guided fractionation was performed to identify potential minor bioactive phytochemicals involved and their botanical sources. Key findings SP (12.5 mu g/ml) and ACR (3 mu g/ml) induced mitotic arrest in both cancer cell models, characterized by an increase in elongated cyclin B1-positive cells, displaying alterations in nuclear and cytoskeleton organization, indicative of a defective spindle assembly checkpoint during metaphase. In contrast, PFR (12.5 mu g/ml) increased cell population at G(0)/G(1) in both cell lines, in comparison to dimethyl sulfoxide control. SP8020-XIV-7 chromatographic fraction induced G(2)/M arrest in treated cells, and Ultra-High Performance Liquid Chromatography-Quadrupole Time-Of-Flight Mass Spectrometry (UPLC-ESI-Q-TOF-HD-MS/MS) analysis revealed that it was composed by naringenin (<1%), kaempferol (23%), kaempferol-3-methyl ether (75%), and an unknown compound [(M-H)(-): 343.0817 m/z, C18H16O7] (<2%), structurally related to eupatorin (G(2)/M inducer), which was additionally identified in ACR. Conclusions We found that phytochemicals from A. confertiflora may contribute to SP bioactivity on cancer cells.