Damping-off, caused by Pythium aphanidermatum and Fusarium solani is a destructive disease of cucumber (Cucumis sativus) worldwide. Application of fungicides and soil fumigation are the common methods of controlling damping-off disease. However, these methods are harmful to humans and the ecosystem. Biological control by using naturally existing antagonistic microorganisms is considered as an environmentally safe method of controlling plant diseases. The objectives of this study were to isolate native antagonistic bacteria from organic compost and to evaluate their ability to promote plant growth and provide protection against P. aphanidermatum and F. solani. A total of 7 bacterial colonies isolated from organic compost were screened for their in vitro antagonism against P. aphanidermatum and F. solani. Among them, two isolates designated as ISO1 and ISO2 showed significant level of antagonism and resulted in an inhibition zone ranging from 5 to 6 mm. Scanning electronic microscopic observation of the mycelium of P. aphanidermatum and F. solani at the inhibition zone showed morphological changes in the hyphae including deformation, shrinkage and loss of turgidity. Based on 16S rDNA gene sequence analysis, both bacterial strains (ISO1 and ISO2) were identified as Pseudomonas aeruginosa. The cell-free culture filtrates of Pseudomonas aeruginosa ISO1 and ISO2 significantly reduced the mycelial growth of P. aphanidermatum and F. solani under in vitro conditions. Compatibility analysis of the bacterial strains using cross-streak assay showed compatibility among them. A greenhouse experiment was conducted to evaluate the effectiveness of the antagonistic bacteria in reducing damping-off disease incidence of cucumber. Both strains were found effective in controlling P. aphanidermatum-induced damping-off of cucumber. Soil application of Pseudomonas aeruginosa ISO1 and ISO2 reduced the yellowing and stunting of cucumber seedlings caused by Fusarium solani. This study demonstrates the effectiveness of Pseudomonas aeruginosa strains ISO1 and ISO2 isolated from organic compost in the management of damping-off of cucumber. It also shows that organic compost has bacteria strains with antagonistic activity against some plant diseases.