This study took Aeromonas hydrophila as an example to study the GGDEF family gene and explore its biological function in Aeromonas hydrophila and its influence on c-di-GMP concentration. In order to systematically study the biological function of GGDEF family genes, 36 strains (54 strains screened by whole genome sequencing) with gene deletion mutation were first constructed, and then phenotypes such as biofilm, crawling and extracellular protease activity were detected. The concentration of c-di-GMP in aeromonas hydrophila was determined by HPLC. At the same time, the deletion strains with GGDEF domain that had a significant effect on the physiological function of Aeromonas hydrophila were screened for mass spectrometry identification, so as to explore the possible molecular mechanism of GGDEF domain protein affecting the physiological function.