Flooding is an environmental stress for plants that not only limits aeration and nutrient acquisition, but also disturbs underground plant-associated fungal communities. Despite frequent flooding, red pine (Pinus densiflora) seedlings thrive in streamside environments. However, whether the compatible ectomycorrhizal fungi (EMF) of red pine are affected by natural flooding is unclear. As EMF are vital symbionts for the development of many trees and allow them to overcome various environmental stresses, in this study, the EMF species associated with red pine seedlings in a streamside environment in Korea were investigated after flooding. The EMF species in 47 seedlings collected from the streamside site were identified by observing their different morphotypes using internal transcribed spacer sequence analysis, and a total of 10 EMF species were identified. The EMF species diversity was lower than that in samples collected from a nearby forest analyzed as a control. The dominant EMF species of streamside seedlings included Amphinema spp., Rhizopogon luteolus, Suillus luteus, and Thelephora terrestris. This study could serve as a basis for investigating the mechanisms by which advantageous EMF aid plant development under flooding stress.