Abstract: Two saline-alkali tolerant and two saline-alkali sensitive rootstocks were used to graft cucumber to determine the effect of saline-alkali stress on microbial community structures in rhizosphere soil of grafted cucumber seedlings. The aim of the study was to explore mechanisms of salt-alkali tolerance of grafted cucumber and promote cucumber cultivation, and further enhance improvement of saline lands. The two saline-alkali tolerant rootstocks were 'Huazhen108' (T1) and 'Shenlitiemuzhen' (T2), the two saline-alkali sensitive rootstocks were 'Huitailang' (S1) and 'Jingxinzhenliuhao' (S2), and then the own-root seedlings of cucumber were used as the control. The physical and chemical properties of soil were adjusted after 10 days of grafted cucumber seedling planting for salinity using 100 mmol·L^-1 mixed salts solution, and the pH adjusted to alkalinity at 9.0. The molar ratio of the mixed salt solution was NaHCO₃︰Na₂SO₄︰NaCl︰Na₂SO₃=4︰2︰2︰0.15. Soils of different treatments were sampled after 30, 40 and 50 days of seedlings planting. And PCR-DGGE technique was used to study microbial community structure and species abundance in rhizosphere soil under cucumber seedlings grafted on different rootstocks. The results indicated that band number in DGGE of saline-alkali tolerant rootstocks was significantly higher than that of saline-alkali sensitive rootstock S2 and own-root cucumber. At the same time, both Shannon-Wiener index and evenness index of rhizosphere soil bacteria of saline-alkali tolerant rootstock T1 were significantly higher than those of the two saline-alkali sensitive rootstocks and own-root cucumber. The number of copies of 16S rDNA gene of bacteria of saline-alkali tolerant rootstock T1 was significantly higher than that of saline-alkali tolerant rootstocks S2 and own-root cucumber after 50 days of growth. The number of copies of ITS gene of fungi of saline-alkali tolerant rootstock T2 was significantly higher than that of saline-alkali sensitive rootstocks and own-root cucumber after 40 days of growth. The number of copies of ITS gene of fungi of saline-alkali tolerant rootstocks was significantly higher than that of saline-alkali sensitive rootstocks, though there was no significant difference between the grafted and own-root cucumber seedlings after 50 days of growth. Cucumber seedlings grafted on different rootstocks had significant differences in both rhizosphere soil microbial community structure composition and species abundance under saline-alkali stress, which became greater with increasing stress time, and changed soil micro-environment. In saline land, saline-alkali tolerant rootstock changed soil environment, and consequently improved grafted cucumber saline-alkali tolerance.