Application of mycorrhizal fungi and salicylic acid (SA) has been found very effective in reducing the adverse affects of drought. Our research examined interaction between seed treatment with 250 µM SA and two mycorrhizal fungi [Funeliformis mosseae (FM) and Rhizophagus intraradices (RI)] under different irrigation levels [100, 70, and 40 % of field capacity (FC)] on photosynthetic pigments, relative water content (RWC), proline content, leaf area (LA), dry weight (DW), phosphorus content, mycorrhizal colonization percentage (MCP) and mycorrhizal dependency (MD) in flaxseed plants during 160 days in 2010–2011. Drought stress reduced LA, plant P, DW, and RWC, but increased soil P, proline content, MCP, and MD, but had no marked effects on plant pigments. In mycorrhizal plants, chlorophyll, LA, RWC, MD, and MCP increased under drought and non-stress condition and RI was more effective than FM on these traits especially under severe drought. Salicylic acid application had positive effect only on MCP and P in the plant under 100 and 70 % FC, while reduced MD, MCP, and plant P at 40 % FC. Moreover, SA application increased LA, plant P, and RWC of non-mycorrhizal plants, but decreased these traits in mycorrhizal plants. In addition, there was antagonistic action between AM fungi and SA. SA may reduce positive effects of mycorrhizal fungi on flaxseed performances under both stress and non-stress conditions. The results suggested that AM inoculation may increase flaxseed growth under both stress and non-stress conditions, while SA application may reduce growth. Moreover, when SA application combines with AM inoculation flaxseed growth may decline suggesting that there may not be synergic effect between these treatments on flaxseed growth.