Stenotrophomonas maltophilia has both negative and positive attributes by being a human pathogen and plant growth promoting rhizobacterium. This study sought to determine if environmental and clinical isolates of S. maltophilia are phenotypically distinct. A total of 18 S. maltophilia isolates from clinical and environmental sources were investigated. Under normal growing conditions, S. maltophila isolates did not enhance growth of canola seedlings. However, under sodium chloride stress (6 decisiemens per meter or 0.33% NaCl), canola seedlings inoculated with S. maltophilia isolates had significantly (P < 0.05) higher number of root branches (isolate D457), root length (D457, CDC 2004-33-01-01 and CDC 2007-23-08-03) and stem length (D457, CDC 2005-37-11-04 and CDC 2011-01-42) than the “no bacteria” control. A number of S. maltophilia isolates protected canola plants from the growth limiting effects of Leptosphaeria maculans and Burkholderia cenocepacia. No clear evidence was found between clinical and environmental isolates based on phenotypic data.