Abstract: Tropical cyanobacterium Cylindrospermopsis raciborskii have attracted much attention due to their rapid expansion into temperate regions. Studies on understanding the genomic characteristics will help analyze their environmental adaptation mechanisms at the molecular level. The genome of C. raciborskii N8 isolated from Zhenhai Reservoir in Guangdong Province was sequenced using PacBio single-molecule real-time sequencing technology, SMRT, and then performed comparative analysis of the whole genomic characteristics. It was shown that genome size of the strain N8 was 3.857 Mb with 40.13% GC content, similar to other 27 C. raciborskii strains in NCBI databases. Further annotation predicted 3598 protein coding genes, representing the largest number among the published genome data. The number of genes annotated in COG, KEGG and GO databases were 2429, 1664 and 2244 respectively. The phylogenetic tree constructed with a single copy gene of the whole genome indicated that C. raciborskii N8 was the most closely related to strain CR12 from Singapore. We inferred that C. raciborskii N8 did not produce toxin cylindrospermopsin (CYN) and saxitoxin (STX) due to the absence of biosynthesis gene cluster for both toxins in its genome. Through examining the genomes of N8 and other 7 strains, we found that these strains had relatively complete phosphorus (P) uptake and transport pathway genes (two-component regulation system, low affinity inorganic P transport gene, high affinity inorganic P transport system, organic phosphonate transport complex, C-P lyase and alkaline phosphatase). This finding demonstrated that C. raciborskii has the potential to utilize different P forms in the ambient environment. However, differences in gene copy number and arrangement among these strains were observed, for example, two C-P lyase complex proteins genes (phnF and phnM) were found in the genome of C. raciborskii N8, while only one in the other 7 strains, indicating variation in C. raciborskii strains. This study represented the first reported whole genome of Chinese C. raciborskii strain. The analysis of its genomic characteristics and P metabolism pathway will help clarify the winning strategies of C. raciborskii in South China.