Organophosphonates, characterized by the presence of a stable covalent carbon-to-phosphorus bond (C-P) represent a class of xenobiotic compounds increasingly entering the environment due to activity of chemical industry. The fundamental knowledge of the mechanisms of biodegradation of organophosphorus compounds containing a C-P bond should serve as a basis of biotechnology for environmental protection and removal of accumulating, toxic phosphonic compounds. Among microbes able to degrade phosphonates via different pathways, fungi play an important role. This review offers analysis of available data on phosphonate-degrading fungi, degradation pathways and regulations of this process.