Phosphonates, comprise a group of organic phosphorus molecules, characterised by a direct C-P bond, rather then the more usual C-O-P bond. Although phosphonates are resistant to both chemical and thermal hydrolysis, there are several bacterial enzymes capable of breaking the C-P bond, and thus liberating inorganic phosphorus. Despite indications that phosphonates comprise 30% of the dissolved organic phosphorus pool in the ocean, little is known of their fate, and research has concentrated on their degradation in oligotrophic environments. However, the quantification and speciation of phosphonate molecules in oceanic environments remained elusive, and although some advances in analytical methodology were made during this thesis, no significant progress was made on the central problem of the extraction of a highly polar analyte with an affinity for divalent cations, from a highly polar, ionic medium. During this thesis, the widespread presence of phosphate-limitation independent phosphonate hydrolase in genomes of marine bacteria, as well as in metagenomic libraries is illustrated, and the presence and expression of some of these genes is illustrated in such diverse marine environments, as coastal ocean, upwellings, coral-associated bacteria and shellfish pathogens. The expression of alkaline phosphatase (AP) was observed in high nutrient upwelling environments and this was linked with the expression of phosphoacetaldehyde dehydrogenase, a phosphonate-degrading enzyme also thought to be under pho regulon control. A possible mechanism involving carbon source activation of the pho regulon under euthrophic conditions is illustrated in the shellfish pathogen, Vibrio Tubiashii, which questions the assumption that DOP utilisation is only important during oligotrophic conditions.