A CBL-interacting protein kinase (CIPK) gene, BnCIPK6, was isolated in Brassing napus. Through yeast two-hybrid screening, 27 interaction partners(including BnCBL1) of BnCIPK6 were identified in Brassica napus. Interaction of BnCLPK6 and BnCBL1 was further confirmed by BiFC(bimolecular fluorescene complemetation) in plant cells. Expressions of BnClPK6 and BnCBL1were significantly up-regulated by salt and osmotic stresses, phosphorous starvation, and abscisic acid(ABA). Furthermore, BnCLPK6 promoter activity was intensively induced in cotyledons and roots under NaCl, mannitol, and ABA treatments. Transgenic Arabidopsis plants with over-expressing BnCLPK6, its activated form BnCLPK6M, and BnCBL1 enhanced high salinity and low phosphate tolerance, suggesting that the functional interaction of BnCBL1 and BnCLPK6 confers Arabidopsis plants hypersensitive to ABA. On the other hand, over-expression of BnCLPK6 in Arabidopsis cipk6 mutant completely resued the low-phosphate-sensitive and ABA-insensitive phenotypes of this mutant, further suggesting that BnCLPK6 is involved in the plant response to high-salinity, phosphorous deficiency, and ABA signaling.