Abstarct: Identification of co-exxpression genes that are effective in salt tolerance in plants and evaluation of their exxpression in biochemical pathways are effective in increasing productivity and development of crop area. In order to investigate the effect of salinity treatment (200 mM) on exxpression of some key genes of lignin biosynthesis pathway (CCR and COMT), their co-exxpression genes (CECCR and CECOMT) and salinity tolerance gene in Soybean (GmSALT3) real-time polymerase chain reaction was used at two time intervals three and seven days after treatment in two salinity resistant and susceptible cultivars. The results of bioinformatics studies showed that different motifs, including GATA-motif, G-Box and TC-rich repeats play important roles in response to different stresses. According to the experimental results, in the resistant cultivar, the exxpression of COMT gene at both time intervals was not significantly different at 5% probability level. In susceptible cultivar, transcxript levels of this gene decreased at both time intervals after treatment, which this difference was significant. In both cultivars, CECOMT gene exxpression decreased at both time intervals when this difference was significant. In resistant cultivar, there was a significant difference in CCR gene exxpression after three days, but no significant increase in CCR gene exxpression after 7 days. Also in susceptible cultivar, the increase of exxpression of this gene was not significant at both time intervals. In both cultivars, CECCR gene exxpression decreased at both time intervals and this difference was significant. Increase in GmSALT3 gene exxpression after three days did not show any significant difference, whereas decrease in exxpression of this gene after seven days showed no significant difference. Also, the increased exxpression of this gene was not significant in both time intervals in susceptible cultivars. According to the results of this study, salinity treatment had a significant effect on the exxpression of genes involved in lignin biosynthesis pathway, its co-exxpression genes and the salt tolerant gene in soybean at three and seven days intervals.