From coastal California seawater, a complex and diverse environment, the marine cyanobacteria of the genus Synechococcus were enriched by flow cytometry-based sorting and the population metagenome was analyzed with 454 sequencing technology. Interestingly, at least three distinct mobile DNA elements not found in model Synechococcus strain genomes were detected in the assembled contigs. These contigs were confirmed to be plasmids. p27638e, p31635e, and p31454e, were sequenced and described. p27638e, p31635e, and p314543e are 1425, 1558, and 1479 kb in length, respectively. Further analysis of natural samples has shed light on their diversity over time. A recombinant plasmid, pTOPO27638 was constructed for sequencing and development of a shuttle vector capable of transforming both Escherichia coli and Synechococcus CC9311. Sixteen presumptive ORFs were identified which may code small peptides. The deduced amino acid sequence of the largest ORFs were significantly similar to that of a putative plasmid replication, repA. Comparison of the replication proteins from p27638e, p31635e and p31454e to other plasmid replication proteins show that it may replicate via rolling circle replication. p27638e and p31635e were found to be positively correlated with marine Synechococcus over time in the environment.