Objective To analyze the genome sequence characteristics of Zika virus and to develop nucleic acid detection methods for Zika virus. Methods The phylogenetic tree of 81 kinds of Flavivirus was constructed. The differences of nucleotide and amino acid sequence among Zika virus, type 4 dengue and Japanese encephalitis virus (JEV) were analyzed and compared. The gene mutated sites of Asian and African Zika virus, especially four Zika virus strains from China, were analyzed. A set of primers and probes of real-time quantitative PCR for Zika virus were designed after comparing the genome sequences of Asian and African Zika virus. Results Spondweni and Kedougou viruses were the closest homologously to Zika virus among 81 kinds of Flavivirus. Comparison of full genomic nucleic acid sequence showed that Zika virus was closer to type 4 dengue virus than JEV, whereas comparison of amino acid yielded an opposite result. Compared with traditional Asian type Zika virus, Guangdong GD01 strains had 5 amino acid mutated sites, Zhejiang ZJ03 strains had 6 mutated sites, and VE Ganxian strains had 33 mutated sites. Detection of designed PCR primers and probes for plasmid RNA was positive, with the lower limit of detection being 100 copies/mL and Zika virus RNA was detected to be positive, type 1-4 dengue virus and Japanese encephalitis virus being negative. Conclusion Zika virus and Spondweni virus are the closest homologously. The high mutation character of VE Ganxian strains indicates that Zika might evolve fast. PCR primers and probes designed in this paper can be used for Asian and African type Zika virus detection, with relatively higher sensitivity and specificity.