Synechococcus sp PCC 7336 represents a newly sequenced strain, and its genome is obviously different from that of other Synechococcus strains. In this analysis, local alignment and annotation databases were constructed and combined with various bioinformatic tools to carry out gene annotation and functional analysis of this strain. From this analysis, we identified 5096 protein-coding genes and 47 RNA genes. Of these, 116 genes that were classified into 9 categories were associated with photosynthesis, and type V polymerase proteins that were identified are unique for this strain. An additional 107 genes were closely related to signal transduction pathways, which primarily comprised parts of two-component regulatory systems. Gene ontogeny analysis showed that 2377 genes were annotated with a total number of 9791 functional categories, and specifically that 41 genes distributed in 4 protein complexes were involved in oxidative phosphorylation. Clusters of orthologous groups classification showed that there were 1463 homologous proteins associated with 17 specific metabolic pathways, and that most of the proteins participated in primary metabolic processes such as binding and catalysis. The phylogenetic tree based on 16S rRNA sequences indicated that Synechococcus PCC 7336 is highly likely to represent a new branch.