One of the fundamental questions of marine biology is what limits the growth of marine organisms? Although there are many environmental variables that may impact on thsis problem, limitation for inorganic nutrients is a key component. Recent examples in the literature provide good evidence for phosphorus (P) limitation of phytoplankton and bacterioplankton growth in several ocean regions. This review seeks to address new molecular methods that may be used to evaluate the P status of bacterial and algal groups in situ. Physiological parameters of the photosynthetic apparatus and cell cycle variables are considered, but attention is focused on the development of protein biomarkers that can be used to derive antibody probes for the immunological interrogation of natural microbial populations. The need to identify suitable protein markers in key genera, and for a good knowledge of the regulation of the marker in the target organism to be obtained before assessing expression in natural populations, is emphasised. We also examine the role of viruses, which are now widely accepted as being abundant in marine environments, as a source of dissolved DNA, and hence an intermediate in P regeneration. Using molecular techniques, we present evidence that the availability of P can influence virus-host interactions, with particular reference to viral lysogeny in marine Synechococcus spp.