Abstract: In this study, we report the cloning and sequencing of M gene of porcine transmissible gastroenteritis virus Fujian strain (TGEV-FJ), and analyze the homology, signal peptide, glycosylation sites, phosphorylation sites, secondary structure of M protein by using bioinformatics software. The complete M gene in TGEV-FJ strain was successfully amplified which has 789 bp, encoding 262 amino acids and then constructed into the recombinant plasmid pGEM-T-M. Sequential analysis and phylogenetic studies demonstrated that the TGEV M gene has highly conservative and consanguineous between TGEV-FJ strain and HN2002 strain. The prediction results showed that M protein in TGEV-FJ strain had a signal peptide cleavage site (ACG16-17ER), and 3 potential N-glycosylation sites,6 serine phosphorylation sites,1 threonine phosphorylation sites and 5 tyrosine phosphorylation sites. The secondary structure of M protein prediction showed that alpha helix, beta sheet and random coil were 11.59%, 44.93% and 43.48%, respectively. The results of the present study would lay some basic molecular biological foundation for prokaryotic expression of M gene in TGEV-FJ strain, which would subsequently facilitate further research for molecular diagnosis and gene engineering vaccines development.