To investigate the effect of flue gas desulphurization byproducts on salinesoil microbial communities,a field experiment with five different levels of flue gas desulphurization byproducts (FGDB) gradient,which were 0,0.74,1.49,2.25,3.00 kg·m-2 respectively,was performed to examine the effect of FGDB on the soil bacteria,ammonia oxidizing bacteria and ammonia oxidizing archaea in 2009 and 2010.The results indicated that FGDB addition resulted in an increase in Ca2+ and NO-3-N and a decrease in pH and electrical conductivity.The results of realtime quantitative PCR showed that the abundance of microbial community composition differed with different FGDB gradient but was nonlinear.Total bacterial 16S rRNA gene copy numbers were significantly higher in FGDB treatments than control.The abundance of ammoniaoxidizing archaea (AOA) and ammoniaoxidizing bacterial (AOB) in T2 and T4 treatments was higher than other treatments.There were no significant differences at 20~40 cm depth for microbial community.The addition of 1.49 kg·m-2 was a threshold value for improving soil bacterial and functional gene abundance.The effects of FGDB on soil microbial community were more effective in top soil than deeper depth.