Phosphonates derivatives are compounds of interests and are applied as drugs of, e.g., antibacterial antiviral activities, connected with their inhibitory activity towards different enzymes, which is related to the configuration of particular compound isomers. The biological synthesis of such molecules is the method of choice and can be carried out using enzymes or whole cells from organisms. Photobiocatalysts employed in the bioconversion of epoxymethyl dimethyl phosphonate are able to convert this substrate into a pure geometric isomer of the unsaturated product, dimethyl (1E)-3-hydroxyprop-1-enylphosphonate, which is a rare and expensive compound of high added value. Six different strains were screened towards dimethyl epoxy phosphonate and in the case of Synechococcus bigranulatus, over 99% conversion was achieved. The product structure was confirmed with Mass Spectroscopy (MS); 1H, 13C, 31P, and 2D Nuclear Magnetic Resonance (NMR); and Infrared Spectroscopy (IR).