Phthalate esters (PEs) are endocrine-disrupting pollutants that are ubiquitous in the environment and can be degraded by microorganisms. In this study, we investigated the kinetics and pathway of biodegradation of di-n-butyl phthalate (DBP), diethyl phthalate (DEP), and dimethyl phthalate (DMP) by cyanobacteria Anabaena flos-aquae G. S. West (strain 4054) and two strains of Microcystis aeruginosa (Kutz.) Kutz. (strain 2396 and strain SM). Gas chromatography/mass spectroscopy (GC/MS) and a deuterium-labeled compound were used to analyze the degrading intermediates. The findings revealed that all three organisms were capable of metabolizing PE, and that among these organisms, A. flos-aquae achieved the highest degradation. Additionally, the biodegradation of DBP, DEP, and DMP followed first-order kinetics. Moreover, the results of the enzymatic study suggested that PE was degraded through transesterification on the side chains rather than deesterification. Finally, experiments using deuterium-labeled DBP showed that there were two degradation pathways: C-16 -> C-14 -> C-12 -> C-10 -> C-8 and C-16 -> C-15 -> C-13 -> C-11 -> C-9. Based on our results, the biodegradation pathway of PE for cyanobacteria was suggested.