Abstract: Objective To understand the genetic diversity of the Campylobacter jejuni strains isolated in China, a high efficient DNA microarray for C. jejuni were designed based on the genome sequences. The increasing released numbers of the released genomes for C. jejuni in these days gave us more information to design the high efficient DNA microarray. Methods A Combimatrix tiling CustomArrayTM (90K chip) were designed according to our previous comparative genomic study. The chip included third sections of the DNA probes. The first section was the probes for the CDSs in the chromosome of the C. jejuni and the second section was the probes for the CDSs from the plasmid. The third section were the probes for the gene clusters related to lipooligosaccharides and polysaccharide capsule biosynthesis. In addition to the whole genome sequence of C. jejuni strain ICDCCJ07001, it included 1579 CDS on chromosome and 37 CDS on the plasmid and 1768 CDSs from other five sequenced strains:269.97, NCTC11168, 81-176, 81-116 and RM1221. The entire 1768 CDSs from five strains were all the strain specific CDSs. All these 3384 CDSs formed the first section probes of the chip. 53 CDSs from a antibiotic resistance plasmids and 37 CDSs from a pathogenicity associated plasmid in C. jejuni formed the second section of the chip. Sixteen and 7 gene clusters related to lipooligosaccharides and polysaccharide capsule biosynthesis respectively were represented in the chip as the third section. The analysis on the distribution of CDSs in different strains and the hierarchical clustering were performed for 27 C. jejuni strains isolated from different sources in China. Results The results revealed that the main hypervariable regions were in the genes clusters related to lipooligosaccharides and polysaccharide capsule biosynthesis, flagellum modification, Campylobacter Mu-like phage as well as DNA restriction and modification. None host attribution feature was obtained by hierarchical clustering analysis of ORF distribution among strains from different sources at genomic level, but the composition of lipooligosaccharides biosynthesis genes of GBS-related strains shared common characteristics based on the component analysis. Conclusion The DNA microarray designed in this study is a useful method to understand the genetic diversity of C. jejuni.