In the present study,two duplicated phospholipase D(PLD) genes,named BnPLDα1(GenBank accession KF113586) and BnPLDα2(GenBank accession KF113587),were cloned by homologous cloning from Brassica napus.Their nucleotide sequences had 87.33％ identity.The predicted amino acid sequence alignment analysis showed that the two BnPLDαs shared 91.01％ identity and most of differential amino acid sites were dispersed,However,the number of differential amino acid sites was up to seven in the sequence that adjacent the first HKD motif which is of crucial importance for the protein’s catalytic activity.In addition,the results of 3-D structure prediction of the two BnPLDαs proteins also show a great difference.Real-time quantitative PCR result showed that all the BnPLDα genes were expressed more in the rapidly growing tissues.The expression of BnPLDα1 was up-regulated,while the expression of BnPLDα2 was unchanged under the low-temperature stress.Under the drought and salt stress,the expression of the two BnPLDα genes both shared the same trend but they rose to maximum effect at different time points,BnPLDα1 in salt stress signal transduction plays a dominant role,but in drought stress signal transduction BnPLDα2 plays a dominant regulatory role.The expression of both BnPLDα genes was down-regulated under the high-temperature stress.These results indicated that BnPLDα1 and BnPLDα2 in the B.napus play a role in defense system that against adversity,but these differences in expression patterns may show their different function from the original gene.