Abstract:he multi-sequence homologous alignment of PipX in cyanobacteria and the conserved sequences were analyzed by bioinformatics softwares and websites such as NCBI,Expasy and so on.The secondary structure and structural domain of PipX was predicted and pipX gene clusters were dissected.The phylogenetic tree of 16S rDNA in cyanobacteria was constructed.In addition,the phylogenetic relationships among PipX,NtcA and PⅡ were studied by constructing phylogenetic trees of these genes.The results indicated that PipX is an important regulation protein in the nitrogen metabolism of cyanobacteria in addition to NtcA and PⅡ,and might have important physiological functions.