Marine Synechococcus spp. are ubiquitous in the marine environment and are known to contribute significantly to primary production. The ecological success of these organisms may be due to the evolution of various genetic lineages physiologically adapted to specific ocean niches. This study focused on one specific physiological attribute, the utilisation and genetic regulation of nitrogen (N) nutrition. Growth data showed no discernable difference in N source utilisation capabilities between marine Synechococcus lineages, but rather a broad utilisation of a range of N sources including ammonium, nitrate, nitrite, urea, and some amino acids. The specific inability of individual strains to utilise urea or nitrate correlated with a lack of genetic capacity to acquire and metabolise these substrates. Such gene loss is likely a function then, of very local environmental conditions 'acting on' a specific strain, rather than a much broader environmental influence on the lineage as a whole.